More than 5,000 names were on the list, sources told CBS, the BBC’s US news partner.

Meanwhile, two lawsuits were filed on Tuesday on behalf of agents seeking to keep the names under wraps.

The developments are the latest struggles over the future of the main US federal law enforcement agency. President Donald Trump believes the FBI and DoJ under Joe Biden unfairly targeted him for prosecution.

Last week, new officials appointed by the White House at the justice department – which oversees the FBI – fired dozens of prosecutors who pursued riot-related cases. Those prosecutors also had worked for special prosecutor Jack Smith, who brought charges against Trump for his alleged role in sparking the riot.

And over the weekend, thousands of FBI employees were asked to fill out a questionnaire about their participation in the Capitol riot investigation – the largest in FBI history.

According to Tuesday’s legal filings, the form included questions such as, “What was your role in the investigation(s) or prosecution(s) relating to events that occurred at or near the US Capitol on January 6, 2021?”

On 6 January 2021, after a speech by Trump, his supporters broke into the US Capitol, delaying the certification of the 2020 presidential election.

Trump effectively ended the investigation into the riot within hours of taking office last month, and pardoned all but a handful of the nearly 1,600 rioters who had been convicted or charged with crimes

One of the lawsuits seeking to stop disclosure of agents’ names alleges that the purpose of the list of FBI employees who worked on the riot and Trump classified documents cases “is to identify agents to be terminated or to suffer other adverse employment action.”

“Donald Trump has made repeated public pronouncements of his intent to exact revenge upon persons he perceives to be disloyal to him,” the filing says.

Lawyers for nine anonymous FBI agents also argue in the filing that revealing details of investigations would harm national security. It says that agents and their families would be “in immediate danger of retribution by the now pardoned and at-large Jan. 6 convicted felons” if their identities are revealed.

A separate lawsuit was filed Tuesday on behalf of another group of seven unnamed agents by the FBI Agents Association (FBIAA) — an organization that represents thousands of current and former bureau employees.

“FBI Special Agents who risk their lives protecting the country from criminals and terrorists are now being placed on lists and having their careers jeopardized simply for doing their jobs,” said FBIAA president Natalie Bara.

Trump’s pick to head the justice department, Pam Bondi, has not been sworn in to her post yet, although that is expected soon after a full Senate vote on her nomination Tuesday.

In the meantime the department is being run by acting chief Emil Bove, a White House appointee who formerly worked as one of Trump’s defence lawyers.

The BBC contacted the justice department for comment on Tuesday’s lawsuits.

The fight over the identities of the FBI agents comes as one of Trump’s top advisors, tech billionaire Elon Musk, sought to stop the disclosure of names of employees in his unofficial Department of Government Efficiency (Doge).

Doge is reportedly attempting to operate in a number of different US government departments. A response to a post on his X network listed several names of Doge employees; Musk replied “You have committed a crime”, and the account posting the original message was suspended.

Other accounts repeated the names, which also were disclosed in news reports.

Thursday’s 88-page report, issued by the office of Inspector General Michael Horowitz, zoomed in on the work of the Federal Bureau of Investigation (FBI), one of the US’s foremost domestic intelligence agencies.

It concluded that the FBI had behaved “effectively” ahead of the attack on January 6, 2021, which sought to disrupt the certification of the 2020 election.

“Despite playing only a supporting role in preparing for and responding to the events of January 6, the FBI recognized the potential for violence and took significant and appropriate steps to prepare for this supporting role,” the inspector general’s office explained.

But, it added, the FBI could have gone further to identify intelligence about potential threats, including by canvassing its field offices for materials, as it does before major events like the Super Bowl.

The FBI, however, has long come under scrutiny for its actions in the lead-up to the January 6 attack.

And the agency’s future is now in question, as its longtime director, Christopher Wray, prepares to step down after more than seven years at the helm.

Incoming President Donald Trump has long taken an adversarial approach to the bureau, which he has described as part of a “deep state” system designed to undercut his authority.

His nominee to lead the FBI, former prosecutor Kash Patel, has floated shuttering the agency’s headquarters in Washington, DC, and significantly reducing its operations.

The report centres on the events of January 6, when Trump, the outgoing president at the time, held a rally near the White House calling on supporters to “stop the steal” of the 2020 election.

He claimed — falsely — that his defeat in the 2020 race was the result of widespread voter fraud.

In the hours afterwards, pro-Trump protesters moved from the Ellipse, a round park south of the White House, to the US Capitol, where members of Congress inside were certifying the election results.

Rioters assaulted law enforcement officers and broke into the Capitol building, some chanting slogans like “Hang Mike Pence”, Trump’s then-vice president. Congress members were evacuated, and one protester was shot and killed as she tried to enter a room through a broken window.

Other deaths have also been linked to the attack. Some protesters suffered medical emergencies during the riot, while several law enforcement officers reportedly killed themselves in the aftermath.

 role the FBI played in the lead-up to those events has been the subject of bipartisan scrutiny in the years since.

A June 2023 report from the Senate Homeland Security and Government Affairs Committee took the stance that the January 6 attack was “planned in plain sight”.

It blamed both the FBI and the Department of Homeland Security (DHS) for “intelligence failures” that allowed the attack to unfurl.

“The intelligence failures in the lead-up to January 6th were not failures to obtain intelligence indicating the potential for violence,” that 2023 report argued.

Rather, it accused the FBI and DHS of failing “to fully and accurately assess the severity of the threat” based on the tips they received.

The report added that both agencies had a duty to issue guidance “with sufficient urgency and alarm to enable” law enforcement “to prepare for the violence that ultimately occurred on January 6th”.

Meanwhile, far-right conspiracy theorists have claimed FBI agents helped spur the violence on January 6, to unfairly smear Trump supporters.

Thursday’s report refutes that. No undercover FBI agents were at the protest, the report says.

While there were 26 confidential informants in Washington, DC, for the events of January 6, only three were at the Capitol, according to the report. It specifies they were tasked with observing “specific domestic terrorism case subjects”, nothing more.

“None of these FBI CHSs [confidential human sources] was authorized by the FBI to enter the Capitol or a restricted area or to otherwise break the law on January 6,” the report explained.

“Nor was any CHS directed by the FBI to encourage others to commit illegal acts on January 6.”

This week’s report also emphasises that the FBI was charged with only a “supporting role” in preparing for the events of January 6.

Rather, it said, law enforcement agencies like the US Capitol Police and the Metropolitan Police Department “were generally responsible for security operations, crowd control, and visitor protection in advance of protests and other demonstrations in and around the Capitol”.