Updated at 3:45 p.m. ET

The Transportation Security Administration withheld N95 masks from staff and exhibited "gross mismanagement" in its response to the coronavirus crisis – leaving employees and travelers vulnerable during the most urgent days of the pandemic, a senior TSA official alleges in a new whistleblower complaint.

On Thursday evening, the Office of Special Counsel, an independent federal agency that handles whistleblower complaints, said it had found "substantial likelihood of wrongdoing" in the complaint and ordered the Department of Homeland Security to open an investigation.

TSA Federal Security Director Jay Brainard is an official in charge of transportation security in the state of Kansas and has been with the agency for almost 20 years.

He told NPR that the leadership of his agency failed to protect its staff from the pandemic, and as a result, allowed TSA employees to be "a significant carrier" for the spread of the coronavirus to airport travelers.

"We did not take adequate steps to make sure that we were not becoming carriers and spreaders of the virus ourselves," Brainard says. "I believe absolutely that that contributed to the spread of the coronavirus."

His allegations include that personal protective equipment was withheld from TSA employees, that local supervisors were not permitted to mandate masks, that the TSA failed to adequately execute contact tracing, and the TSA declined to require that employees change or sanitize gloves between passengers.

The coronavirus crisis hit during one of the nation's busiest traveling times: spring break.

"You've got communities shutting down. You've got governors shutting things down. And we still hadn't mandated masks. We still hadn't mandated eyewear. We still weren't changing personal protective equipment as often as we needed to," Brainard says. "Every federal security director was forced to fend for him or herself."

The Department for Homeland Security, TSA's parent organization, did not respond to a request for comment. Office of Special Counsel spokesperson Zachary Kurz told NPR: "OSC cannot comment on or confirm the status of open investigations."

Brainard says that in mid-March, he and other security directors at TSA asked for help on masks and were rebuffed. When Brainard asked whether he could mandate his workforce wear masks, he was told this was not permissible.

"Every effort was made to convince our leadership to give us the latitude to roll out personal protective equipment. That didn't happen at that point," Brainard says.

When another federal security director asked in a March 12 email if the TSA could provide N-95 respirators masks they had in stock to employees, the request was denied without explanation.

"There are NO surgical masks available for purchase nor have any been sent to us. Employees are unable to acquire their own. Officers are now asking when they can have masks. We have N95 Masks in inventory. May they be issued to requesting officers?" Federal Security Director Robert Krekorian asked senior TSA leadership, in an email shared with NPR.

"While we understand the situation, at this time, you cannot issue N-95s," came the response, adding that additional masks would arrive by the end of that month.

"Waiting two or more weeks for them may be too late," Krekorian wrote back.

To date, TSA says 695 agency employees have tested positive for the coronavirus, and five employees have died as a result. In addition, one screening contractor has died because of COVID-19.

Publicly, the TSA's leadership suggested that they were adequately prepared for the pandemic.

On March 3 at a Senate hearing, TSA Administrator David Pekoske said he believed that the TSA had what it needed to handle the coming crisis, and that the TSA would provide surgical masks to its employees.

"I do feel we have the resources and the capability," he said. "If [screening officers] would like to wear a surgical mask, they're permitted to do that and we provide those masks."

But Brainard charges that the TSA's leadership was actually woefully slow to react.

Brainard says it was not until almost a month after he and others began raising questions that local leadership was allowed to mandate workers wear masks, and not until June that the TSA's security officers were required by agency officials to wear a mask.

In an emailed response to NPR, TSA said wearing masks was optional for officers in the checkpoint area until the first week of May. Eye protection is still optional, according to TSA, but gloves are required.

"TSA requires frontline personnel to wear nitrile gloves when conducting screening duties. They are to change their gloves after each pat-down. Travelers may request new gloves to be used at any time during the screening process," a TSA spokesperson told NPR.

NPR reached out to several TSA federal security directors, who said the policy had been that gloves are changed between pat-downs only in the specific situation when an alarm is set off. The TSA announced Friday, following the publication of NPR's story, that passengers would now be allowed to request TSA screeners change their gloves.

The number of passengers traveling through American airports dropped dramatically at the onset of the coronavirus crisis but is beginning to pick back up.

Brainard says that even now, more than three months after the president declared a state of national emergency, the response is lacking.

"The bottom line is the new procedures in place do not adequately address the prevention of the spread of the coronavirus," he told NPR.

He said that a "belated" set of procedures issued by the TSA did not have guidance or mandatory safeguards on protective eyewear, temperature checks or the sterilization of gloves between interactions with passengers.

The Office of Special Counsel's finding that there was "a substantial likelihood of wrongdoing" in Brainard's allegations means that the Department of Homeland Security must now conduct an investigation into the allegations within 60 days, although an extension is possible. The letter explaining that finding was shared with NPR by Brainard's lawyers.

The results of the investigation will then be sent back to Brainard for comment, and the final results shared with Congress and the White House and released to the public.

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