Acting US Deputy Attorney General Emil Bove made the statements on Wednesday in a memo to staff seen by Reuters.
"Let me be clear: No FBI employee who simply followed orders and carried out their duties in an ethical manner with respect to January 6 investigations is at risk of termination or other penalties," he wrote.
"The only individuals who should be concerned ... are those who acted with corrupt or partisan intent."
The Justice Department is set to square off in court on Thursday against FBI employees who have sued to protect the identities of agents who investigated Donald Trump supporters in the storming the US Capitol on January 6, 2021.
The two lawsuits by agents and other FBI personnel said up to 6000 FBI employees participated in the investigations.
The attack on the Capitol was an unsuccessful effort to overturn Trump's 2020 election defeat.
In his memo on Wednesday, Bove said he demanded the names of all FBI employees who worked on January 6 cases only after the bureau's acting leadership "refused to comply" with a request for the names of core Washington-based January 6 investigators.
That act of "insubordination" led him to demand the much broader list, he said.
A spokesperson for the FBI did not immediately respond to a request for comment on the memo.
Bove on January 31 fired eight top FBI officials and demanded information about every FBI employee who worked on the January 6 cases by Tuesday.
The FBI provided the list on Tuesday but it listed staff by their employee number rather than name.
