The embattled former FBI director, James Comey, has formally called on a judge to dismiss the government’s “vindictive and selective prosecution” against him, accusing President Trump of directing a retaliatory case and claiming the new, interim U.S. attorney overseeing the case was “invalidly appointed.”

“The indictment in this case arises from multiple glaring constitutional violations and an egregious abuse of power by the federal government,” Mr. Comey’s attorneys wrote in a 51-page motion filed Monday.

In their motion, Mr. Comey’s attorneys said the former FBI director and longtime Trump nemesis had been singled out for prosecution “because of his protected speech and because of President Trump’s personal animus” toward him. 

“President Trump’s decision to unlawfully manipulate the prosecutorial process for the express purpose of bringing a charge against Mr. Comey proves that his animus was the but-for cause of this prosecution,” his attorneys wrote in their motion.

“The proper remedy for this unconstitutional prosecution is dismissal with prejudice,” his attorneys added.

In September, Mr. Comey was charged with making a false statement and obstruction in Senate Judiciary Committee testimony in which he denied authorizing an FBI employee to “be an anonymous source in news reports” about the FBI’s investigations into both Mr. Trump and Secretary Hillary Clinton. He has pleaded not guilty.

In a separate motion, Mr. Comey’s attorneys said the “unlawful appointment” of Mr. Trump’s former defense attorney and White House special assistant, Lindsey Halligan, as the interim U.S. attorney for Eastern Virginia rendered the indictment a “nullity.”

Mr. Comey’s attorneys highlighted a Truth Social post made, and later deleted, by Mr. Trump in which he implores the attorney general, Pam Bondi, to ramp up efforts to prosecute Mr. Comey as well as New York’s attorney general, Letitia James, and Senator Adam Schiff, a Democrat of California. 

“We can’t delay any longer, it’s killing our reputation and credibility. They impeached me twice, and indicted me (5 times!), OVER NOTHING,” Mr. Trump wrote.

Ms. Halligan pursued a grand jury against Mr. Comey days before the five-year statute of limitations on Mr. Comey’s alleged offenses were to expire. 

“No other prosecutor from the U.S. Attorney’s Office for the Eastern District of Virginia participated in the grand jury presentation. Ms. Halligan presented the grand jury with a three-count indictment,” Mr. Comey’s attorneys wrote. Mr. Comey was ultimately charged with two criminal counts.

Ms. Halligan advanced criminal charges against Mr. Comey and Ms. James after her predecessor, Erik Siebert, was forced out after Mr. Trump objected to the strong support he had from Virginia’s two Democratic senators. Mr. Siebert was also reportedly resisting pressing charges against Ms. James. Last week, Ms. Halligan fired two lawyers in her office over  their resistance to pursuing charges against Ms. James, who was ultimately charged with bank fraud and making false statements to a financial institution. 

In a court filing Sunday, prosecutors raised concerns over Mr. Comey’s lawyer and former U.S. attorney for the Northern District of Illinois, Patrick Fitzgerald, citing a 2019 justice department OIG report that highlighted Mr. Fitzgerald’s possible involvement in efforts to share a sensitive memo with the press. 

Prosecutors also asked U.S. District Judge Michael Nachmanoff to advance their request for a “filter team” of attorneys to review electronic evidence related to Mr. Comey’s case to confirm what role, if any, Mr. Fitzgerald played in disseminating material to the media.

“This fact raises a question of conflict and disqualification for current lead defense counsel. Some of the communications in the potentially protected material are from the same time as the focus of the DOJ OIG report,” prosecutors wrote in its motion filed Sunday. 

In 2019, Inspector General Michael E. Horowitz’s report “found no evidence that Comey and his attorneys released any of the classified information contained in any of the memos to members of the media.”

In response, Mr. Comey’s defense attorneys, including Mr. Fitzgerald, said there was no good-faith basis in attributing criminal conduct to either Mr. Comey or Mr. Fitzgerald, adding that the government’s efforts to “defame” Mr. Fitzgerald has no grounds for the motion’s granting. 

“There was no ‘leaking’ of classified information to the press by either Mr. Comey or his counsel. Full stop,” Mr. Comey’s attorneys wrote in their response.

On Monday night, Judge Nachmanoff denied the government’s request for an expedited filter team protocol.