The Department of Veterans Affairs has drastically scaled back the use of hydroxychloroquine to treat veterans with coronavirus infections after a major study raised questions about its efficacy and linked it to serious side effects, including higher risks of death.

Testifying before the House Appropriations subcommittee on military construction, Veterans Affairs and related agencies, VA Secretary Robert Wilkie defended the continued use of the unproven drug but said it was used just three times last week.

“We have ratcheted down as we’ve brought more treatments online,” Wilkie, who wore a surgical mask, told the panel. “And I expect that to continue.”

At the height of its use, VA prescribed the drug to 404 patients the week of March 29, agency data shows.

The most high-profile proponent and user of hydroxychloroquine is President Trump, who has heralded the antimalarial drug as a treatment “game changer” and asked patients “What do you have to lose?” by taking it. The president said he was taking it himself as a prophylactic but has since said he has stopped.

White House press secretary Kayleigh McEnany said at a news conference Thursday that Trump was “feeling perfect” after taking the drug and would take it again if he thought he was exposed to the disease.

“It’s important to note that this drug has been safely used by millions of people for a long time,” she said.

Anthony S. Fauci, the country’s top infectious-disease expert, said Wednesday on CNN that “the scientific data is really quite evident now about the lack of efficacy.”

Fauci’s remarks came on the heels of a global study that concluded the drug was linked to significantly higher risk of death and irregular heart rhythms when used for coronavirus treatment.

Participating by teleconference, Appropriations Committee Chairman Nita M. Lowey (D-N.Y.) told Wilkie: “I hope VA would respond to the science that is clearly coming from Dr. Fauci, rather than some wishful thinking from the president.”

VA has issued the drug to 1,300 patients suffering from covid-19, the disease caused by the novel coronavirus, the agency told Senate Minority Leader Charles E. Schumer (D-N.Y.) in a letter last week.

A retrospective, non-peer-reviewed study by VA and academic researchers of 368 patients at VA hospitals showed that the drug had no benefit in treating coronavirus patients and was linked to higher rates of death. More than 27 percent of patients who received the drug had died, versus 11.4 percent who died with no drug regimen, the study said.

The number of patients receiving the drug has declined since late March. But the largest weekly drop, 78.8 percent, occurred after the VA-focused study was published online. A VA spokesman did not return a request for comment on whether the study played a role in that drop.

The Food and Drug Administration, in a safety alert issued April 24, warned that it had received reports that hydroxychloroquine and chloroquine could have serious side effects and that the drug should be taken under the close supervision of a doctor in a hospital setting or a clinical trial.

“We are all learning as we go,” Wilkie said of the drug’s use, including consultations he has had with Fauci as late as this week. Both officials serve on the White House’s coronavirus task force.

Wilkie said that after peaks of use in a crush of patients, VA has scaled back use of the drug as other treatments, such as remdesivir and convalescent plasma, have become more common.

But unanswered questions about VA’s continued use of the drug still linger among veterans advocates.

Jeremy Butler, the chief executive of Iraq and Afghanistan Veterans of America, said the agency has not publicly addressed the barrage of studies showing elevated risk and has not provided updates on patient outcomes since the VA study was made available last month.

“VA seems to adamantly want to avoid saying they think it was a bad idea,” Butler said after watching Wilkie’s testimony. “They’re still using it as an open question while evidence is to the contrary.”

Hydroxychloroquine is commonly prescribed at VA hospitals for lupus and rheumatoid arthritis, and VA doctors administer the drug only after ensuring patients and caretakers know its risks, a common practice with other treatments and drugs, agency spokeswoman Christina Noel said. But she has not addressed questions about whether new studies have prompted a reevaluation of the department’s drug policy.

“It makes you wonder what they’re saying when they’re having consultations with patients,” Butler said of Wilkie’s testimony.

The Veterans of Foreign Wars said on May 1 it was “very disturbed” VA was administering the drug, and it called on the agency to halt its use. The group on Thursday said Wilkie and VA have been more transparent about the drug since then.

At least 1,200 veterans have died of covid-19, VA said Thursday, although that is an undercount. At least 614 veterans have died at state-run veterans homes, Vietnam Veterans of America said Thursday, though only 19 states are publicly and fully reporting the number of dead in those homes, the group said. VA figures do not include them, Noel has said.

Felicia Sonmez contributed to this report.