For weeks, nurses and other employees at Veterans Affairs hospitals have said they were working with inadequate protective gear. VA officials denied it.

But in an interview, the physician in charge of the country’s largest health-care system acknowledged the shortage — and said masks and other supplies are being diverted for the national stockpile.

“I had 5 million masks incoming that disappeared,” said Richard Stone, executive in charge of the sprawling Veterans Health Administration. He acknowledged that he’s been forced to move to “austerity levels” at some hospitals.

Stone said the Federal Emergency Management Agency directed vendors with equipment on order from VA to instead send it to FEMA to replenish the government’s rapidly depleting emergency stockpile.

FEMA has responded to President Trump’s decision to invoke the Defense Production Act to boost supplies as governors have made frantic requests for masks, ventilators, medical gowns and other supplies, depleting the stockpile.

VA’s four-week supply of equipment — on the shelves of 170 medical centers and in an emergency cache normally used for hurricane responses — was almost gone, and employees have held protests to say they were not safe. The system was burning through about 200,000 masks in a day, Stone said.

“The supply system was responding to FEMA,” said Stone, a former combat surgeon and former Army deputy surgeon general. “I couldn’t tell you when my next delivery was coming in.”

The shortages, and the agency’s claims that they did not exist, have been a low point in what observers say is an otherwise commendable response by VA to the pandemic. The health system, with fewer covid-19 patients than it expected, is now reaching out to assist veterans in troubled state facilities.

“They have to manage hundreds of thousands of employees, and what’s clear to me is that VA is not insulated” from resource shortages, said Rep. Mark Takano (D-Calif.), chairman of the House Veterans’ Affairs Committee. “My frustration is I wanted to know their guidance to the field. We couldn’t find out.”

After an appeal from Secretary Robert Wilkie to top FEMA officials, the emergency management agency provided VA with 500,000 masks this week, FEMA said in a statement. It did not address questions about the agency’s diverted equipment orders. A similar shipment arrived last week, Stone said. It’s allowed him to loosen the mask policy to provide employees working directly with covid-19 patients with one face mask a day.

Still, hospitals in the sprawling system have discretion to ration equipment if they are treating large numbers of covid-19 patients and face shortages. In a recent memo, a top health system official told regional directors they should plan for “scenarios that permit extended mask use, permit limited re-use, permit staff to bring in their own facemasks and N95 respirators, and allow decontamination of used N95 respirators.”

The American Federation of Government Employees, which represents hundreds of thousands of VA workers, says nurses are still struggling and are often given surgical masks and face shields instead of the N95 respirators that are more effective at limiting contagion.

The Labor Department says it is investigating a union complaint at one hospital that employees suspected of contracting the virus were ordered to continue to report to work. On Thursday, several Senate Democrats, describing a “broken federal procurement and distribution process,” called on the Trump administration in a letter to Vice President Pence to get more supplies to VA hospitals.

Barbara Galle, an intensive care nurse at the Minneapolis VA hospital who is president of AFGE Local 3669, said staff caring for covid-19 patients still can only get an N95 mask if they are involved in a procedure that puts them at extra risk of breathing in virus droplets in the air, she said.

Other hospital workers, including pharmacy technicians and cafeteria workers who deliver food to patients on covid wards, have been told to wear their masks for a week, she said. If the straps break, they must staple them back together.

The hospital’s prosthetics department just started producing 3-D-printed masks, she said — and its pharmacy is now making 3-ounce bottles of hand sanitizer for the medical staff.

Her biggest frustration is that VA did not level with employees sooner.

“Everyone functions at their best if they have knowledge of the situation and what’s going on,” Galle said.

VA serves a vulnerable veteran population dominated by older, Vietnam-era men with underlying health conditions. The system mobilized early in the crisis, restricting visitors to its nursing homes, screening veterans and others entering hospitals and turning its health-care system into a series of acute-care, covid-19 wards.

Stone began a national effort to recruit nurses from schools and from the community of VA retirees to bulk up his medical staffs, some of which have long struggled with vacancies. The system created training videos to teach nurses assigned to non-emergency settings the skills they would need in intensive care units.

He told hospital staffs that some of them would likely be asked to take temporary assignments at medical centers with a surge in coronavirus cases. The health system added 3,000 intensive care beds to augment its supply of 10,000. Wilkie told FEMA and the Department of Health and Human Services that he had 1,400 open beds to offer to treat civilians with the virus.

The system prepared for an onslaught to its emergency rooms as computer models suggested the virus could hospitalize as many as 200,000 of the 9 million veterans in VA’s system.

The numbers so far have fallen far short of that estimate. The number of VA patients with covid-19 hit 6,300 in recent days, with 400 deaths.

About 1,900 health-care workers have become sick with the virus, the agency said, with 20 deaths. About 3,600 of the health-care staff are now quarantined after exposure.

Stone said the system was able to start testing the staff for the coronavirus only in recent weeks. While VA’s pandemic response plan predicts that as many as 40 percent of employees could be absent from work for illness or fear of the virus, the absentee rate across the health system has hovered at about 4 percent during the pandemic, Stone said, slightly below normal rates.

Stone and Wilkie sat side-by-side under fluorescent lights on a recent day with a handful of colleagues as they prepared for a daily conference call with regional leaders in the hospital system. Most are veterans themselves.

A panel of digital screens stretched along a wall in front of them, the coronavirus tracking tools anchoring what has become a 24-hour pandemic nerve center at VA’s headquarters in downtown Washington.

The surveillance models superimposed the virus’ penetration across the country on the locations of VA hospitals, allowing officials to see what may lie ahead for veterans. Pink circles hovered over the current hot spots of the Bronx and Brooklyn in New York, Boston, Chicago, New Orleans, Detroit, the District and Baltimore.

The models tracked available beds in each hospital, the median days veterans spend as inpatients, their ages. Bed occupancy overall was at 40 percent. One statistic stood out: Of all covid-19 fatalities in the U.S. so far, one out of five is a veteran over 70.

Yet the system has not been overwhelmed. Wilkie, pointing to a map of the country, noted that a relative few veterans have been hospitalized in the Great Plains and the West.

“We don’t have a lot going on west of the Mississippi,” he said. “We’re just not overwhelmed with patients. Could it come? Yes.”

VA’s regional directors began reporting in on a 3:30 p.m. call. The head of Region 5 in the Mid-Atlantic said, “Our positives are about the same.” Region 10, covering Ohio, thanked colleagues in three other areas of the country for sending ventilators, extra staff, testing kits and other reinforcements. Region 12 in the Great Lakes said, “Chicago’s really getting hit hard.”

Region 17 out of Texas said “mask demands are increasing” and made clear that it’s eagerly awaited a shipment on the way of nasal swabs to test for the virus. Region 20, covering the Pacific Northwest, was down to a two-week supply of protective equipment.

Wilkie told the staff he had some good news: The White House coronavirus task force was likely to recommend a resumption of elective surgeries where possible.

Then came the first signs of what would turn out to be VA’s next mission. The regional leaders said they were starting to get frantic calls from the staff at many state-run nursing homes for veterans. The homes were desperate for help, as the virus was spreading through and killing dozens of veterans.

Before the pandemic, VA’s backup role to treat an overflow of nonveterans from private hospitals or other facilities was little known outside the veterans community. It’s known as the Fourth Mission. Few states had asked for the agency’s help, though, beyond a few hundred beds, most in the stricken New York and New Jersey area.

The reasons are unclear. Health and Human Services, which is supposed to field requests for backup assistance, referred questions to FEMA. An agency spokeswoman referred questions to “individual states.”

VA decided to reach out to other vulnerable veterans. In the last week, the health system has lent its support to the troubled state system of veterans homes. The homes are not run by the federal government, but VA gives them financial assistance — and has now offered to treat dozens of their patients in its hospitals.

About 50 veterans from homes in 11 states are now being treated for covid-19 at VA hospitals, officials said. About 90 nurses have deployed to two New Jersey homes with virulent outbreaks.

The flexibility is made possible by a surge in hiring by VA, which was able to circumvent the government’s byzantine hiring rules during the emergency and bring on 3,200 new employees in the last month. Almost 1,000 are registered nurses.

On Friday, the nurses union continued its protests over protective gear shortages, forming a picket line in front of hospitals in Florida and Georgia, two states whose governors have announced that they are reopening for business during the pandemic.