An independent federal watchdog has ordered an investigation into the Transportation Security Administration’s response to the coronavirus, after a whistleblower alleged that the agency botched its initial handling of the pandemic when millions of people continued to fly each day, and that it is still doing too little to protect travelers and its own employees.

The whistleblower, Jay Brainard, the top TSA manager in Kansas, filed his complaint with the Office of Special Counsel, saying the agency’s failures amounted to “gross mismanagement.”

“I and my counterparts have tried to convince them to do what’s necessary to protect the public,” Brainard said in an interview. “I don’t know why they ­haven’t done it.”

According to a letter shared with The Washington Post, the special counsel’s office told Brainard and his lawyers on Thursday that it had directed the Department of Homeland Security to open an investigation into some of his allegations, meaning it has determined they are credible.

The TSA has issued new standard operating procedures for protecting against the virus that went into effect last week and has publicly announced changes to its screening procedures. But Brainard and his lawyers at the Government Accountability Project say they contain gaps — including no procedures for handling travelers who appear to be sick — that leave the public in danger.

“We’re very concerned that they’re so weak and incomplete,” said Tom Devine, legal director for the Government Accountability Project. “They’re going to institutionalize the TSA workforce as a major threat for spreading the pandemic.”

The Office of Special Counsel does not conduct its own investigations. But once the DHS internal investigation is complete, the office will review it and determine whether the review and any corrective action are reasonable. The office will then share its findings with the president, Congress and the public.

“While OSC has found a substantial likelihood of wrongdoing based on the information you submitted in support of your allegations, our referral to the Secretary for investigation is not a final determination that the allegations are substantiated,” the office wrote to Brainard on Thursday.

Zachary Kurz, a spokesman for the special counsel’s office, said he could not confirm or comment on open investigations. DHS did not respond to a request for comment.

“All guidance from TSA has been in accordance with CDC guidelines,” Lisa Farbstein, a TSA spokeswoman, said in an email.

In Brainard’s complaint, memos he sent members of Congress during the spring, and other documents shared with The Post, he describes how the TSA struggled to respond to the coronavirus even as it rapidly spread through the agency’s own workforce. As early as March 23, agency employees in 11 states had fallen ill, and workers in an additional 30 states were in quarantine, according to a map the agency produced.

As the virus continues to spread, 695 TSA employees have fallen ill; five have died, as has a contractor, the agency says.

In its referral to DHS, the special counsel’s office said the department should investigate Brainard’s allegations that the TSA has not provided pandemic-related training, that the new procedures don’t require officers to use protective eyeware or use hand sanitizer between passengers, and that the agency has not installed plastic barriers to separate officers and passengers.

Farbstein confirmed that use of eyewear remains optional but said officers are required to change gloves after pat-downs. Passengers can also request that they change their gloves, she said. Farbstein sent photos of barriers installed at Reagan National Airport.

Brainard’s allegations about the TSA mirror complaints from unions and Democratic lawmakers that the federal government had done too little to prepare the aviation system as a whole for a pandemic — despite a 2015 Government Accountability Office report spelling out the gaps in planning. Lawmakers have called on the government to set national standards for social distancing, mask usage and other safety precautions on planes and at airports, but officials have not taken action.

Air passenger numbers collapsed in late March and April, as governors imposed stay-at-home orders to slow the spread of the virus. But as air travel slowly starts to rebound, the TSA has been rolling out new approaches to safety. It has encouraged social distancing and has changed screening procedures to reduce the number of physical bag searches by requiring passengers to separate food from their carry-on luggage.

Brainard alleges that the agency is still not doing everything it could to keep passengers and screening officers safe. He blamed a lack of planning by agency leaders and an overreliance on local officials to make decisions.

“The air transportation system is like a football stadium with 440 doors in it,” Brainard said, referring to the number of airports where the TSA has operations. “If you’re going to protect that stadium, you need to protect those entrances.”

Brainard has spoken out against the agency’s leadership repeatedly in recent years, testifying before a congressional committee in 2016 that top officials were “some of the biggest bullies in government.”

The coronavirus began to take hold in the United States as the TSA was preparing for a rush of spring break travelers. The agency initially refused to allow its officers to wear N95 masks, despite internal lobbying by field leaders and public calls from their union for better protection.

On March 12, the TSA field director in New Hampshire sent an email asking senior officials managing the coronavirus outbreak whether he could issue N95 masks to his employees, which were understood at that time to offer protection against the virus, even though officials were not recommending the use of face coverings more generally.

He was told no.

“How do we justify the denial of personal protection to our front line officers in this environment when we have N95 masks,” the field director, Robert C. Krekorian, wrote back. “The nature of their work makes ‘Social Distancing’ virtually impossible.”

At the same time, the TSA was hoarding more than 1 million N95 masks that were in short supply elsewhere in the federal government, said Chuck Kielkopf, an agency lawyer based in Ohio. Kielkopf filed a complaint with the special counsel’s office, first reported by ProPublica. But he said Monday that the office declined to take it up, telling him the issue “was within the discretion of TSA leadership.”

Meanwhile, the masks continue to go unused.

“You can always make a case that you need to have them,” Kielkopf said. “It’s kind of like stocking up on toilet paper. Do you really need a year’s worth of toilet paper?”

The TSA announced in early May that it would require screening officers to wear masks and internally circulated its revamped screening procedures on May 13, delaying their implementation for a month. But Brainard’s complaint alleges that officers have not received any pandemic-specific training and are not getting enough guidance from leaders at the agency’s headquarters.

Field directors have been working to install clear plastic shields — a step the Centers for Disease Control and Prevention recommended for businesses in early April — at some locations. But on May 23, Assistant TSA Administrator Gary Renfrow wrote in an email that the agency was still trying to procure the shields centrally and told field officials that “if you haven’t already installed your own solution, please hold on for just a bit for a common solution.”

The new procedures require TSA officers to change their gloves every 30 minutes, but in his complaint, Brainard said that in that time officers could come into contact with 50 passengers.

Brainard said that he recognizes the pandemic is unprecedented but that the TSA should nonetheless have been better prepared for the outbreak.

“We have been in existence since 2001, so 19 years. At what point did we plan for this?” he said. “There have been plenty of opportunities to take a look.”