Funds for vital health programs around the world remain frozen and their work has not been able to resume, despite a federal judge’s order that temporarily halted the Trump administration’s dismantling of the government’s main foreign aid agency.

Interviews with people working on health initiatives in Africa and Asia found that parents in Kenya whose children are believed to have tuberculosis cannot get them tested. There is no clean drinking water in camps in Nigeria or Bangladesh for people who fled civil conflict. A therapeutic food program cannot treat acutely malnourished children in South Sudan.

“We have people traveling 300 kilometers from the mountains to try to find their medications at other hospitals, because there are none left where they live,” said Maleket Hailu, who runs an organization that assists people living with H.I.V. in the Tigray region of Ethiopia and relied on funding from the United States Agency for International Development. “U.S.A.I.D. was providing the medications and transporting them to rural places. Now these people are thrown away with no proper information.”

A State Department spokesperson said on Tuesday that the office of Secretary of State Marco Rubio had issued more than 180 waivers permitting lifesaving activities to resume, and that more were being approved each day. The department did not reply to a request to provide a list of the 180 projects.

But even programs with waivers are still frozen, according to people in more than 40 U.S.A.I.D.-funded groups, because the payments system that U.S.A.I.D. used to disburse funds to the organizations has not operated for weeks. Without access to that money, programs cannot function.

On Thursday night Judge Amir H. Ali of the U.S. District Court for the District of Columbia denied a motion to hold the Trump administration in contempt of court for continuing to freeze aid, recognizing that the government had acknowledged that “prompt compliance with the order” was required.

But he wrote that the restraining order “does not permit Defendants to simply continue their blanket suspension of congressionally appropriated foreign aid,” in order to have time “to come up with a new, post-hoc rationalization for the en masse suspension.”

Organizations usually receive their grants in small increments, by submitting requisitions for activities they will imminently carry out. They rely on that quick turnaround to keep operating. Many of the groups affected are nonprofits that have no other source of funds.

“Some N.G.O.s have received waivers, but waivers without money are just pieces of paper — and you can’t run programs with just paper,” said Tom Hart, the chief executive officer of InterAction, which represents 165 organizations that deliver foreign aid. “These organizations haven’t been paid for work dating back to December, and they have zero assurance they’ll be paid for that work or any work going forward.”

Speaking at a meeting with aid organizations last week, Peter Marocco, the Trump appointee who is now the director of the Office of Foreign Assistance at the State Department, said the payment system was offline but would be restored by Feb. 18. It has not been.

Mr. Marocco signed a declaration submitted to the judge in the federal court, reporting on the government’s compliance with the restraining order. In it, he argued that the administration was acting based on other regulations, not the executive order, to continue to freeze funding.

The Trump administration insists that the waiver system is allowing emergency work to continue unfettered. But the process of issuing the exemptions has been complex, the State Department spokesperson said, because the department has had to verify that organizations seeking them are not misrepresenting their activities.

“The department found that many activities that have previously been described as lifesaving humanitarian assistance have in reality involved D.E.I. or gender ideology programs, transgender surgeries, or other non-lifesaving assistance and efforts that explicitly go against the America First foreign policy agenda set forth by the president,” the statement said.

U.S.A.I.D. did not fund gender transition surgery; programs that had a gender focus included efforts to protect women from domestic violence and prevent H.I.V. infection in vulnerable teenage girls.

Organizations that have received waivers report that one or two activities in larger projects were approved to restart, while the surrounding and related activities are still frozen.

The chief executive of a large organization providing health care who asked not to be identified because he was barred from speaking with the news media by the U.S.A.I.D. stop-work order, said his agency had received two of 24 waivers for which they applied. If the organization had all the waivers, they would cover about five percent of its activities. So far it has received no funds. “I can’t buy medications with a waiver,” he said.

The Elizabeth Glaser Pediatric AIDS Foundation is the only organization The Times has found in an extensive survey of U.S.A.I.D. recipients that has resumed work after receiving a waiver.

But the foundation has not been able to access any new money. To restart its H.I.V. testing and treatment programs, it has used money it had received as repayment for disbursements before the stop-work order, said Trish Karlin, the organization’s executive vice president. She said the foundation received waivers for 13 of its 17 projects.

“For awards where we are not funded by advances but rather are paid in arrears after we invoice the U.S. government, we have not been paid and are due almost $5 million,” she said.

Karoun Demirjian contributed reporting.

Three buses exploded in Tel Aviv area parking lots on Thursday night, raising suspicions of an attempted, coordinated terrorist attack and prompting the Israeli authorities to halt all buses and trains nationwide. There were no injuries reported.

After the explosions, Prime Minister Benjamin Netanyahu’s office said in a statement that he had instructed the military to carry out “a massive operation” in the West Bank targeting militant hubs and had ordered the police and intelligence forces to step up preventive measures in Israeli cities to thwart any subsequent attempted attacks.

The three buses were parked at different depots in Bat Yam, a city south of Tel Aviv, Tzvika Brot, the city’s mayor, said in a statement. Unexploded bombs were also found in parking lots in the nearby city of Holon, the mayor noted.

Mr. Brot said he had ordered additional security patrols throughout Bat Yam. “The city will remain on high alert throughout the weekend,” he added. “However, the city’s routine continues as usual. There is no change to school tomorrow or any other activities.”

Ofir Karni, director of the Dan bus company, told Israeli news media that the last passenger on one of the buses that exploded had noticed a suspicious bag on a back seat and had alerted the driver. They drove into the depot, got off the bus and it exploded after they exited, he added.

The series of explosions in central Israel came on what was already a difficult day for Israelis and for the country’s tenuous truce with Hamas.

Four coffins said to contain the remains of hostages, including two children, who were captured from a community near the Gaza border in the Oct. 7, 2023 Hamas-led attack, were released and repatriated for burial on Thursday. But the Israeli military said in a statement early on Friday that only three of the bodies belonged to the hostages slated to be handed over.

One of the bodies it received could not be identified, it said, adding it did not belong to Shiri Bibas — the mother of the two children handed over — and did not match the identity of any other hostage. The military called the issue a “violation of utmost severity” of the cease-fire terms.

The attempted bus attacks around Tel Aviv, which no one has yet claimed direct responsibility for, could also undermine mediators’ efforts to get Israel and the militant group to negotiate the next phase of the cease-fire.

Since late January, the Israeli military has been conducting intense raids in the Israeli-occupied West Bank, saying it is trying to root out Hamas and other militant groups.

The operation across several West Bank cities has displaced roughly 40,000 Palestinians from their homes, making it the biggest displacement of civilians in the territory since the Arab-Israeli war of 1967, according to historians and researchers.

The military has destroyed houses and ripped up roads in what it has said is an effort to uncover improvised explosive devices. The operations have killed dozens of Palestinians, according to both the Israeli and Palestinian authorities.

Defense Minister Israel Katz directed the military to intensify those operations in refugee camps in the West Bank in response to the attempted attacks on Thursday.

“We will chase after the terrorists and destroy the terror infrastructure — whoever provides cover for terror will pay a heavy price,” he said in a statement.

A West Bank arm of Hamas’s military wing, the Qassam Brigades, issued a statement that appeared to praise the explosions but did not explicitly claim responsibility for them.

The Israeli military said in a statement late on Thursday that it was working with intelligence authorities and the police to investigate the incident in Bat Yam. It said that “intensified antiterror activity” in the West Bank was continuing, and that it had blocked entry to certain parts of the territory “accordingly.”

Bus and train service in Israel will remain paused until the police and intelligence authorities’ give directives that it can resume, according to a statement from the transportation ministry.

Johnatan Reiss, Fatima AbdulKarim, Isabel Kershner and Aaron Boxerman contributed reporting.

The Trump administration on Thursday transferred all of the Venezuelan migrants it had brought to the U.S. military base at Guantánamo Bay, Cuba, suddenly emptying a detention operation that it had just as abruptly started this month.

Two passenger planes operated by Global X, a charter aircraft company, flew to the naval base on Thursday morning and shuttled most of the migrants to an airfield in Honduras. They were to then be put aboard a Venezuelan plane for repatriation.

Tricia McLaughlin, a spokeswoman for the Homeland Security Department, said 177 migrants had been transferred to Venezuelan custody, and one had been brought back to an immigration facility in the United States. In a declaration filed in court earlier on Thursday, an Immigration and Customs Enforcement official had said 178 Venezuelans were at the base.

It was unclear whether the administration intended to send additional migrants to the base.

The transfers cleared out the migrants at a time when the operation has raised numerous questions about whether the government had legitimate legal authority to take people from ICE facilities in the United States to the base in Cuba for continued detention. Immigrant rights’ lawyers have gone to court seeking access to the migrants, and rights groups have been expected to file a broader challenge to the Trump administration’s policy.

“It’s a way to avoid litigation from getting traction,” said Harold Hongju Koh, a Yale Law School professor who worked as a lawyer in the State Department during the Obama administration has long been involved in litigation over detainees at Guantánamo. He added: “Possession is nine-tenths of the law.”

The turnover took place at the Soto Cano air base, where the U.S. military’s Southern Command has maintained a presence for decades, a statement from Honduras said.

The Honduran government said it was facilitating the transfer for what it described as humanitarian reasons.

On Jan. 29, Mr. Trump directed the U.S. military and the Homeland Security Department to prepare to expand a migrant operations center at Guantánamo Bay, saying it would “provide additional detention space for high-priority criminal aliens unlawfully present in the United States.”

The military began transporting migrants to the base on near daily flights from an immigration site in El Paso, starting on Feb. 4. In announcing the first transfer flight, the Pentagon cast the operation as a “temporary measure” to secure the migrants “until they can be transported to their country of origin or other appropriate destination.”

All of the migrants taken to Guantánamo to date have been citizens of Venezuela. It has been difficult to deport people to the country because of the breakdown in relations between its authoritarian government and the United States.

But a Trump adviser, Richard Grenell, visited Venezuela in late January and appeared to achieve a diplomatic breakthrough, which included an agreement that Venezuela would resume accepting deportees. On Feb. 10, Venezuela sent two planes to El Paso to pick up about 190 of its citizens, whom the Homeland Security Department described as under final deportation orders.

As the flights resumed, it has not been clear why some Venezuelans were taken to Guantánamo.

Trump administration officials had initially portrayed the migrants taken to Venezuela as members of the Tren de Aragua gang, which the State Department included on a list of transnational cartels and gangs the administration designated as foreign terrorist organizations on Thursday.

But it is not clear whether that is true for any of the migrants: Congressional staff were told in a briefing that the only actual criteria to be sent to the base was being Venezuelan with a final removal order.

As of Wednesday, Ms. McLaughlin, the homeland security spokeswoman, had said simply that ICE was using Guantánamo “to house detainees subject to final orders of removal.” She also referred to them as “final order aliens.”

In a lawsuit seeking legal access to the migrants, the government told a court that it had allowed three men named in the suit to call lawyers on Monday and that “preliminary access procedures have been developed for others at the facility.”

But the Justice Department also urged a judge not to require broader access, arguing that the migrants had only “limited rights” as “immigration detainees with final orders of removal, who are staged for final transfer and in the midst of a removal operation.”

The Trump administration has raised the possibility of eventually housing tens of thousands of migrants at the base. With the future of the policy unclear, Lee Gelernt of the American Civil Liberties Union, the lead lawyer for the immigrant rights’ groups seeking access to migrants at Guantánamo, said the fight was far from over.

“The government saying we can now have access to the detainees only after they have moved them is perplexing, at best,” he said. If the government was trying to make the lawsuit moot, he added, “they will not succeed.”

Eric Schmitt contributed reporting from Washington, and Albert Sun from New York.

The two tiny redheaded boys had captured the hearts of Israelis and became symbols of the long and emotional campaign for the release of the scores of hostages seized during the Hamas-led attack on Oct. 7, 2023.

On Thursday, under gray, stormy skies, an anguished nation marked an unofficial day of mourning after Hamas handed over three black coffins that the group said bore the remains of Ariel Bibas, who was only 4 when he was taken captive to the Gaza Strip; his baby brother, Kfir Bibas, who was not even 9 months old at the time; and their mother, Shiri Bibas, who was 32.

A fourth coffin bore the remains of Oded Lifshitz, an octogenarian grandfather, a peace activist and a founder of the pastoral Israeli village of Nir Oz, near the border with Gaza, where he and the Bibas family resided.

All were alive when taken.

At a grotesque handover ceremony in Gaza on Thursday morning, with loud music blaring in the background, the coffins were put on display on a podium bearing images from family photos that were also used in Israel for hostage posters: Ariel in a little white polo shirt; Kfir with a wide, toothless grin clutching a bright pink cuddly toy; and Shiri Bibas, smiling and radiant before the family’s world fell in.

The masked gunmen, though, appeared to have mixed up the children’s pictures and names.

By sundown on Thursday, Israel’s National Center of Forensic Medicine and the Israel police had still not completed the identification process of the remains. Only Mr. Lifshitz’s body had been positively identified.

Yarden Bibas, Ms. Bibas’s husband and the children’s father, was abducted separately during the Oct. 7 assault, bleeding from a head wound. He was released alive this month as part of the cease-fire between Israel and Hamas that came into effect in January.

But the fate of the rest of his family has tormented Israelis, underscoring what many here view as the cruelty of Hamas.

“Dear citizens of Israel, on this day we are all united in grief that is too heavy to bear,” Prime Minister Benjamin Netanyahu said on Thursday, in a somber message to an aching nation. “Today, every home in Israel bows its head.”

A month after the war set off by the Hamas attack began, the group’s armed wing, the Qassam Brigades, claimed that Ms. Bibas and her two children had been killed in an Israeli airstrike. Fears grew in Israel when they were not among the other captive mothers and children released during a weeklong cease-fire that month.

But the Israeli authorities had not confirmed their deaths, let alone the circumstances, saying only that there was “grave concern” over the hostages’ fates.

Relatives held out hope until the very end.

After Hamas announced on Tuesday that it would release the Bibases’ remains, the family expressed anger over the early eulogizing in the news media of Ms. Bibas and the children before Israel had even determined that they had been killed.

Should we receive devastating news, it must come through the proper official channels after all identification procedures are completed,” the family said in a statement on Wednesday.

The Israeli government did not immediately provide details of the cause of Mr. Lifshitz’s death, but said he had been “murdered in captivity” by Islamic Jihad, a smaller Palestinian armed group that has been holding a number of hostages.

Hamas turned over the bodies as part of a series of negotiated exchanges in the first phase of the cease-fire agreement. In recent weeks it has released 19 living Israeli hostages.

The agreement provides for the release of 33 Israeli hostages in exchange for more than 1,500 Palestinian imprisoned in Israel during the first phase, which, barring an extension, is set to expire in early March.

The Israeli government said last month that Hamas had provided a list indicating that 25 of the 33 hostages were alive and that eight had been killed.

Roughly 1,200 people were killed in the Hamas-led 2023 attack and more than 250 abducted, according to Israel. Nir Oz was one of the hardest-hit communities, with about a quarter of its 400 residents either killed or taken hostage. Kfir was the youngest to be seized.

The attack prompted Israel to declare war on Hamas and invade Gaza in a 15-month military campaign that has killed tens of thousands of Palestinian civilians and combatants and left much of the coastal enclave in ruins.

On Thursday, groups of Israelis stood in the rain and held silent vigils along the route as coffins bearing the hostages’ remains were transferred from Gaza to the National Center of Forensic Medicine in Tel Aviv.

Eylon Keshet, Mr. Bibas’s cousin, described Ariel in November 2023 as a boy who loved being the center of attention and playing with toy tractors and cars. Kfir, he said, was a “chill” baby who was just beginning to eat solid food.

The Hostage Families Forum, an organization advocating for the hostages and their families, described Ms. Bibas in a statement as “a dedicated mother and accountant, known for her boundless kindness.”

“They weren’t just names,” the forum said of the deceased hostages, adding, “They were beloved people, with families who cherished them, with dreams and futures stolen from them.”