The complaint is heavily redacted, with few details on the allegations, but it is the latest indication that there are internal concerns about the top U.S. diplomat's behavior, two months after he had the department's inspector general fired.
Pompeo has dismissed similar reports before, blasting questions about his involvement in politics before a trip to Iowa last week, where he met with social conservative leaders and local politicians in the key battleground state.
According to the complaint, the whistleblower said they "directly" observed the activity, along with other staffers who "tried on several occasions to obtain clarifications and guidance from senior leadership in S/ES (the secretary's executive secretariat) and from the Office of Legal Advisors, but were blocked from doing so."
The activity took place in Washington, D.C.; New York, Florida, and possibly elsewhere in the U.S.; and overseas, the complaint said. Only one allegation is not redacted -- "false or misleading statements" -- although it's unclear who the charge is filed against.
While senior department figures "were made aware of these concerns on repeated occasions," the whistleblower told the Office of the Inspector General, which recorded the complaint, "none of them ever took action to resolve the issues, and several of them specifically directed subordinate staff to continue facilitating questionable activities after the concerns were raised."
The State Department did not respond to a request for comment.
Pompeo had President Donald Trump fire the department's inspector general Steve Linick in May, later citing concerns about him or his office leaking to the press -- an allegation Linick denied in congressional testimony.
At the time, the OIG was investigating Pompeo's role in the use of an emergency authority to bypass Congress and sell Saudi Arabia and the United Arab Emirates $8 billion in arms and his use of staff to run personal errands for him and his wife.
Pompeo has denied that Linick's firing was retaliation, at first saying he was unaware of any investigations and then saying while he answered questions about the arms sale probe, he didn't know the full scope.
"Someone was walking my dog to sell arms to my dry cleaner. I mean, it's all just crazy," he said in May.
It's unclear if those two probes are related to the behavior described in the complaint, which was released to the left-leaning watchdog group American Oversight as part of a Freedom of Information Act lawsuit.
At least some of the information that is redacted is because there is an ongoing investigation into it, according to a letter from the OIG's acting counsel to American Oversight.
Pompeo's tenure has come under increased scrutiny in recent months -- especially after Linick's firing -- and focused on his own political future.
While he long denied he was running for an open Senate seat from Kansas, four trips to his adopted home state last year fueled speculation. Sen. Bob Menendez, D-N.J., even requested a probe into the trips, which later cleared Pompeo because he ultimately never ran.
But Pompeo has been more open about his presidential ambitions, and some critics have accused him of using meetings on overseas trips or dinners at the department for the wealthy and powerful to lay the groundwork for a White House run.
During a visit to Iowa, which holds the nation's first contest for each party's nominee, Pompeo met behind closed doors with "Iowa business leaders," "local leaders," "elected officials," and "members of the Iowa Farm Bureau," according to his public schedule.
He, his wife Susan, and their son Nick also attended the Family Leadership Summit, a social conservatives gathering that's influential in the Republican Party, where Pompeo attacked "rioters" tearing down statues and mayors not keeping Americans safe.
Asked about the political nature of that visit two days earlier, Pompeo told "The Hill" that he wanted to visit "America's heartland."
"Every American ought to hear from America's secretary of state about our foreign policy, about our trade policies that affect the people of Iowa greatly," he added, without addressing the moderator's question about a 2024 presidential run.