The lead federal prosecutor who helped uncover massive fraud in Minnesota has resigned from the U.S. Attorney's Office.

Joe Thompson served as the acting U.S. Attorney of Minnesota after being appointed by President Donald Trump in May 2025. He led the office until Daniel Rosen took over as U.S. attorney in October.

"It has been an honor and a privilege to represent the United States and this office," Thompson, 47, wrote in an email obtained by the Minnesota Star Tribune.

A New York Times report said that Thompson and other prosecutors resigned over the Justice Department's approach to the investigation of the fatal shooting of Good, but a DOJ official told Fox News Digital that the prosecutors had submitted early retirement paperwork months earlier, which preceded the shooting death of Good. They remain on the job until their retirement date, the official said.

A source familiar with the situation told Fox News that Thompson said on phone calls with DOJ colleagues that he believed the shooting was justified.

The department defended its handling of the investigation.

"There is currently no basis for a criminal civil rights investigation," Deputy Attorney General Todd Blanche said in a statement provided to Fox News Digital about the probe into the shooting.

"As with any officer-involved shooting, each law enforcement agency has an internal investigation protocol, including DHS," a DOJ official told Fox News Digital. "As such, ICE OPR has its own investigation underway. This runs parallel to any FBI investigation."

Thompson was the lead prosecutor that helped uncover the massive $250 million Feeding Our Future food fraud case tied to the state's Somali community.

The fraud has resulted in dozens of indictments and convictions, as well as shining a spotlight on fraud concerns in Minnesota. Minnesota Gov. Tim Walz chose not to run for a third term amid the widening scandal.

"Our state is far and away the leader in fraud now and everyone sees it," Thompson told the Minnesota Star Tribune Editorial Board last year.

In addition, Thompson was involved in several other high-profile cases, including filing federal charges against Vance Boelter for his alleged shooting rampage that killed Minnesota state Rep. Melissa Hortman and her husband, Mark, and seriously wounded Minnesota state Sen. John Hoffman and his wife, Yvette, according to the newspaper.

Aside from Thompson, at least four senior lawyers at the Justice Department's Civil Rights Division resigned in recent days, Reuters reported Tuesday.

The departures were prompted in part by a decision to sideline their unit from investigating the shooting death of Good, according to two sources familiar with the departures. The DOJ said those reports are false.

Harmeet Dhillon, who heads the division and was appointed by Trump, informed the unit last week they would not be involved in the probe, one of the sources said. The sources spoke on the condition of anonymity to discuss a sensitive internal matter.

On X, she called reports of the resignations "bogus."

"Fake news media, foiled again!" she wrote. "The news of "mass resignation" was bogus, and now debunked. We have lots of work to do!"

The Trump administration said Good was trying to ram a U.S. Immigration and Customs Enforcement (ICE) officer, while critics contend she was trying to get away from authorities. (Fox News)