A senior official at the main U.S. aid agency, which is being dismantled by the Trump administration, told employees to clear safes holding classified documents and personnel files by shredding the papers or putting them into bags for burning, according to an email sent to the staff.

The email sent by Erica Y. Carr, the acting executive secretary, told employees of the U.S. Agency for International Development to empty out the classified safes and personnel document files on Tuesday. “Shred as many documents first, and reserve the burn bags for when the shredder becomes unavailable or needs a break,” Ms. Carr wrote, according to a copy of the email obtained by The New York Times.

The agency has fired thousands of employees, put some on paid leave and asked a few to work from home, so the headquarters have been mostly empty for weeks.

It is unclear if Ms. Carr or any other official at U.S.A.I.D. got permission from the National Archives and Records Administration to destroy the documents. The Federal Records Act of 1950 requires U.S. government officials to ask the records administration for approval before destroying documents.

The documents being destroyed could have relevance to multiple court cases that have been filed against the Trump administration and the aid agency over the mass firing and sudden relocation of employees, the rapid dismantlement of the agency and a freeze on almost all foreign aid money.

The State Department and a spokesperson for U.S.A.I.D. did not respond to requests for comment.

The American Foreign Service Association, a union representing career diplomats that is a plaintiff in a lawsuit, said in a statement on Tuesday that it was “alarmed by reports that U.S.A.I.D. has directed the destruction of classified and sensitive documents that may be relevant to ongoing litigation regarding the termination of U.S.A.I.D. employees and the cessation of U.S.A.I.D. grants.”

“Federal law is clear: The preservation of government records is essential to transparency, accountability and the integrity of the legal process,” the union said. “We call for full adherence to federal records preservation laws to ensure accountability and protect the rights of U.S.A.I.D. employees.”

The union also noted that employees engaged in the improper destruction of records could find themselves in legal jeopardy.

The aid agency employs nearly 2,000 career diplomats, known as Foreign Service officers, and they are represented by the union. Diplomats generally destroy large numbers of documents only when an embassy or other post is about to be overrun by a hostile force. Some diplomats who got Ms. Carr’s email on Monday night called union officials after becoming anxious over the sudden request.

The Federal Records Act says that “agencies must follow retention schedules approved by” the records agency and covers all electronic documents as well. Printed documents must be saved in an electronic format before being destroyed, and the act says that “agencies must manage electronic records effectively, ensuring accessibility and security.”

In some federal agencies, employees regularly destroy physical documents after saving them in electronic form. It is unclear if employees at U.S.A.I.D. have ensured that all physical documents are being saved electronically before being destroyed.

In her email, Ms. Carr asked employees to meet at 9:30 a.m. on Tuesday in the lobby of the Ronald Reagan Building, where the U.S.A.I.D. headquarters is housed, to take part in the destruction of documents. The U.S. government has ended the agency’s lease for office space there. Secretary of State Marco Rubio, who is the acting administrator of the agency, plans to move the remnants of U.S.A.I.D. into the State Department after firing thousands more employees.

The email told employees to mark burn bags with “SECRET” or “USAID/(B/IO)” with a dark Sharpie if possible. “B/IO” stands for bureau or independent office.

Mr. Rubio took charge of U.S.A.I.D. last month and announced that Pete Marocco, a divisive appointee at the State Department, would oversee day-to-day operations. Mr. Marocco has worked with young employees of a task force run by Elon Musk, the billionaire adviser to President Trump, to halt the disbursement of foreign aid funds, cut contracts and fire thousands of employees or put them on leave.

In a volatile cabinet meeting at the White House last Thursday, Mr. Rubio vented his anger at Mr. Musk for the eradication of the aid agency.

On Monday, Mr. Rubio announced on social media that officials had canceled 5,200 aid agency contracts, or 83 percent of the total. The remaining 1,000 will be managed by the State Department, he said. And he thanked Mr. Musk’s team.

The State Department has not released details of the remaining 1,000 contracts.

Several hundred employees of U.S.A.I.D. will probably be absorbed into the State Department, aid agency officials say.

A federal judge ordered the Trump administration on Monday to restart aid payments for work that had been completed. The judge noted that Congress had appropriated foreign aid funds, and that the Trump administration did not have the right to “impound” the money. An executive order signed by Mr. Trump on Jan. 20 froze almost all foreign aid funding.

Ryan Mac contributed reporting from Los Angeles.

Dalvin Modore walked as if there was broken glass beneath his feet, stepping gingerly, his frail shoulders hunched against the anticipation of pain. His trousers had become so loose that he had to hold them up as he inched around his small farm in western Kenya.

Mr. Modore has tuberculosis. He is 40, a tall man whose weight has dropped to 110 pounds. He has a wracking cough and sometimes vomits blood. He fears the disease will kill him and has been desperate to be on medication to treat it.

Mr. Modore is one of thousands of Kenyans, and hundreds of thousands of people worldwide, with TB who have lost access to treatments and testing in the weeks since the Trump administration slashed foreign aid and withdrew funding for health programs around the globe.

Many, like Mr. Modore, have grown significantly sicker. As they go about their lives, waiting and hoping, they are spreading the disease, to others in their own families, communities and beyond.

The whole system of finding, diagnosing and treating tuberculosis — which kills more people worldwide than any other infectious disease — has collapsed in dozens of countries across Africa and Asia since President Trump ordered the aid freeze on Jan. 20, Inauguration Day.

The United States contributed about half of international donor funding to TB last year and here in Kenya paid for everything from nurses to lab equipment. Trump administration officials have said that other countries should contribute a greater share to global health programs. They say administration is evaluating foreign aid contracts to determine whether they are in the national interest of the United States.

While some of the TB programs may ultimately survive, none have received any money for months.

Family members of infected people are not being put on preventive therapy. Infected adults are sharing rooms in crowded Nairobi tenements, and infected children are sleeping four to a bed with their siblings. Parents who took their sick children to get tested the day before Mr. Trump was inaugurated are still waiting to hear if their children have tuberculosis. And people who have the near-totally drug-resistant form of tuberculosis are not being treated.

Mr. Modore shares a bed with his cousin and his home with four other relatives. All of them have watched him get sicker and thinner, fearing also for their own health.

Despite being fully treatable, tuberculosis claimed 1.25 million lives in 2023, the last year for which data is available.

The main TB research effort, testing new diagnostics and therapies, has been terminated. The global procurement agency for TB medications lost its funds, then was told it might regain them, but still has not. Stop TB, the global consortium of government and patient groups that coordinates tuberculosis tracking and treatment, was terminated, had the termination rescinded, but still has received no funds.

The United States did not pay for all the TB care in Kenya, but it funded critical pieces. And when those were frozen, it was enough to bring the entire system to a halt.

The United States paid for motorbike drivers, who earned about $1 for transporting a sample taken from a person with a presumptive infection to a lab to test it for TB. The drivers were fired on the first day of the funding cut — so the transportation of samples stopped.

The United States paid for some laboratory equipment used to process tests. In many places, processing stopped.

The United States paid for the internet connectivity that allowed many testing sites to send results back to far-off patients via local community advocates known as TB Champions. So even when patients found a way to send samples to a working lab, notification of results stopped.

Without testing that confirms whether a person is infected and what type of TB they have, family members cannot start on preventive therapy.

The United States paid for the half-dozen tests that patients need before beginning treatment for multi-drug-resistant TB, to make sure their bodies will be able to tolerate the harsh drugs. These tests can cost $80 or more, beyond the reach of many patients. Without the tests, clinicians don’t know what drugs to prescribe very sick patients. Prescriptions stopped.

The United States paid for the ships and trucks that moved drugs to ports and on to warehouses and clinics. Shipments stopped.

And the United States paid for the data management contract that provided a national dashboard of data on cases, cures and deaths. Tracking stopped.

Evaline Kibuchi, the national coordinator for the Stop TB Partnership in Kenya, predicted that it would take only three months before infections and deaths from TB increased. “But we won’t even know about the new deaths, because all the data collection was supported by U.S.A.I.D.,” she said.

The United States also paid the stipends — about $35 a month — of community health workers, and TB Champions, who lost the tiny salaries that belie their vital role. Research has shown that because TB treatment involves taking drugs for many months, often with miserable side effects, patients are much more likely to finish a course of medication and be cured when someone is checking on them regularly, cheering them on and watching for lapses.

But across Kenya, the community advocates have kept working, unpaid, covering the costs of trying to reach patients and delivering diagnoses out of their own pockets.

Mr. Modore’s constant cough drew neighborhood attention in January. Doreen Kikuyu, the TB Champion in his area, came and collected a sputum sample from him and used the motorbike system to send it for diagnosis.

By the time his results came back, the Trump administration had frozen the system. Ms. Kikuyu could not get funds for a motorbike to take her to his home to inform him. “But I could not leave him without knowing the answer,” she said. “So I set out walking.”

She also explained that the lab analysis did not provide information on whether he had a drug-resistant form, so he would need further testing before he could start the proper medication. But he would have to pay 1,000 Kenyan shillings — about $8 — to send a sample to the regional laboratory that could do this test. To pay for it, they might need to sell a chicken, one of their few assets. They debated what to do as the days ticked by.

“I’m really hoping to start on medication but I’m just left wondering what will happen,” Mr. Modore said one recent afternoon, sitting hunched in the shade of a stand of trees outside his house.

Eventually, the intrepid Ms. Kikuyu managed to scrape together the money, by gathering contributions from other now-fired community health workers and neighbors. She sent the sample to the lab. Good news came back: Mr. Modore did not have drug resistance and could take the standard medications.

But there was no one to prescribe them. The staff members at the clinic were paid by the United States, and they were now fired. Ms. Kikuyu was at her wit’s end, knowing Mr. Modore was desperately ill.

Working her phone, using airtime she bought herself, she badgered a local government TB official who is a clinician to meet her at the hospital and to prescribe and issue the drugs from the shuttered clinic storeroom. She scraped together more money to bring Mr. Modore to the clinic on a motorbike. As she watched him grin and take his first pills, she felt a flood of relief.

But immediately, she faced a new worry: His family and close neighbors, about a dozen people, needed to start preventive therapy to protect them from getting sick too. The clinic is closed. If she can find a clinician to prescribe drugs for the adults, at least, she could deliver them. (TB drugs for children are complex and require a doctor’s supervision.) But she’s out of money to get back to the Modore home. She has worn herself out walking to the homes of other patients who are waiting for tests, waiting for results, waiting for drugs.

“It’s a problem,” she said wearily. “But we have to get to that family.”

For TB treatment to work, patients must take their drugs every day, without interruption, for months.

Barack Odima, a 38-year-old mechanic in Nairobi, has the most deadly form of the disease, one that is resistant to most treatments. Last fall he started on a rare drug combination, but when he went to pick up his medication two weeks ago, the clinic staff told him that one of the drugs had not been restocked and that they had nothing for him.

“If I don’t get this drug that is missing, how will I be cured?” Mr. Odima said.

After another week, the clinic received a small batch of medications. The clinician and the pharmacist had been laid off, so a TB Champion gave him the medication — but could not tell him how many more pills he might receive.

While he is on the drugs, Mr. Odima is supposed to have monthly testing of his blood, liver and kidneys to make sure his body is tolerating them. That costs about $80, previously covered by the U.S. grant, and he has not had a test since the funding freeze. Mr. Odima’s wife and five children are supposed to be rechecked for the disease this month; it will take all his savings to pay for X-rays.

In an interview in a clinic treatment room plastered with stickers and posters advertising U.S.A.I.D. support, Mr. Odima said he was grateful to the United States for assisting with his treatment, but was baffled that the country had cut off help. Of course his own government should provide such care, he said. “But we are a dependent country,” he said, “and Kenya is not able to support the programs so that all the people with these diseases can get cured.”

In truth, the TB treatment system in Kenya was none too sturdy before the United States yanked its support — the country had nearly 90,000 new infections last year. Labs ran short of supplies to do molecular tests, and people were often misdiagnosed.

The TB Champions, who drop in to check in on anyone they hear about with a persistent cough, were intended as a low-budget, high-impact strategy to change that. Since the aid freeze, they have taken on outsize importance. In the scruffy western Kenyan town of Busia, a Champion named Agnes Okose is using the money she earns from her snack stall to fund trips to outlying villages. Since late January, she has been delivering diagnoses and collecting sputum samples in plastic sample jars she buys herself, toting them in a small lunch cooler to a laboratory in town.

“I am a TB survivor myself: I cannot leave people just dying,” she said. “Whatever small-small money we can find, we are using it.”

The aid cuts have also crippled a network of clinics set up all over Africa two decades ago by President George W. Bush’s Emergency Plan for AIDS Relief. Those clinics bypassed the frail, bureaucratic and graft-riddled health systems in countries battling TB and H.IV. and put patients on lifesaving medication quickly. Twenty years later, they were still partly or totally separate, in most places, and had U.S.-paid staff.

Now African health officials are scrambling to absorb those patients into the regular medical system — as many as 40 percent more people to care for, in facilities that were already overstretched. Kenya’s national government has said it is working on a plan but offered no details for how it will bridge the yawning funding gap.

But because all the TB and H.I.V. cases have gone to the separate clinics for years, clinicians in the main facilities don’t know about drug protocols, side effects or signs of treatment failure.

“You will have health care workers who have never seen a TB case; there will be quality-of-care issues,” said Dr. Timothy Malika, who oversees the TB program of Kisumu County, which has one of the highest rates of TB infection in Kenya.

Abigael Wanga, who lives in a village in Busia County, has five children; two have taken TB treatment for a year. But the two children, Philemon, 8, who hopes to be a pilot one day, and his headstrong sister Desma, 3, still have chest pain and coughs, and no appetite.

Ms. Okose fears they are drug-resistant. She collected sputum samples from them and their three siblings the day before the inauguration. The testing is frozen, and all five children continue to sleep under one blanket at night.