Adam Cohen, who was director of the Organised Crime Drug Enforcement Task Forces, in a social media post said he had been fired by Deputy Attorney-General Todd Blanche, Trump's former criminal defence lawyer who was confirmed to the department's number two role by the US Senate on Wednesday.
Cohen's firing came just 18 hours after Blanche released a memo that Cohen had helped him draft which announced that the taskforce he led would be playing a new leading role in combating illegal immigration, as part of an initiative dubbed "Operation Take Back America".
"It was a shock," Cohen wrote of his firing on LinkedIn, noting he had been meeting regularly with leadership to discuss violent crime initiatives.
"Putting bad guys in jail was as apolitical as it gets," he wrote.
"My personal politics were never relevant. Not until yesterday."
Cohen's firing is one of the latest examples of the Trump administration removing or sidelining career Justice Department officials, who typically keep their positions across presidential administrations.
Also on Friday, three assistant US attorneys in the Southern District of New York, including two who were involved in prosecuting the corruption case against New York Mayor Eric Adams, were placed on administrative leave, according to an internal email by acting US Attorney Matthew Podolsky that was seen by Reuters.
Their removal comes after eight Justice Department attorneys in Washington and New York resigned in protest after refusing to file a motion to dismiss the corruption charges against Adams.
The email identified the prosecutors involved in Adams' case as Celia Cohen and Andrew Rohrbach.
"We were given no notice, nor asked for our views on this decision, with which I disagree," Podolsky wrote.
"On that case and others, Celia and Andrew did the right thing, for the right reasons, in the right way - every single day."
A third prosecutor, Alex Kristofcak, was also placed on leave in response to comments he made on social media, the email said.
In those comments, Kristofcak criticised Washington, DC's interim US attorney, Ed Martin, after he warned Georgetown University Law School that he would not hire its students unless the school removed diversity, equity and inclusion from its curriculum.
"This is a grotesque abuse of power," Kristofcak wrote of Martin.
"I am so sorry for my colleagues in DC who have this thug of a boss."
A spokesman for the US Attorney's Office in the Southern District of New York declined to comment.
Other career department officials were also fired Friday, including pardon attorney Liz Oyer and Bobak Talebian, who oversaw the handling of Freedom of Information Act requests.
