WASHINGTON — Accusing the Justice Department of a “gross abuse of prosecutorial power,” a former mafia prosecutor and retired federal judge urged a court on Wednesday to reject the Trump administration’s attempt to drop the criminal case against Michael T. Flynn, President Trump’s former national security adviser.

“The government has engaged in highly irregular conduct to benefit a political ally of the president,” wrote John Gleeson, who was appointed to a special role to argue against the Justice Department’s unusual effort to drop the Flynn case. He added: “Leave of court should not be granted when the explanations the government puts forth are not credible as the real reasons for its dismissal of a criminal charge.”

But Mr. Gleeson also argued in a 73-page brief that Mr. Flynn should not be held in criminal contempt of court for lying under oath when he gave conflicting statements about his actions. Instead, he wrote, the federal judge overseeing Mr. Flynn’s case, Emmet G. Sullivan, should take that behavior into account when imposing a sentence on Mr. Flynn.

The Justice Department “has treated the case like no other, and in doing so has undermined the public’s confidence in the rule of law,” Mr. Gleeson wrote. “I respectfully suggest that the best response to Flynn’s perjury is not to respond in kind. Ordering a defendant to show cause why he should not be held in contempt based on a perjurious effort to withdraw a guilty plea is not what judges typically do.”

The brief was the first response in the case from Mr. Gleeson, whom Judge Sullivan appointed last month to help him analyze Attorney General William P. Barr’s request to dismiss the case against Mr. Flynn, who had twice pleaded guilty to a charge of lying to the F.B.I. The move was highly unusual and prompted an outcry among former law enforcement officials that the administration was further politicizing the department.

The Justice Department argued that Mr. Flynn’s lies were not “material” to any legitimate investigation — rejecting the department’s previous position that his lies were relevant to the counterintelligence inquiry into the scope of Russia’s covert operation to tilt the 2016 election in Mr. Trump’s favor and the nature of links to Trump campaign associates.

Mr. Gleeson, who had co-written an Op-Ed article calling into question the legitimacy of Mr. Barr’s intervention before Judge Sullivan appointed him, offered a blistering critique of that rationale, saying “no federal prosecutor worth her salt” would adopt the “legally unsound” conclusion the Justice Department put forward.

“Pursuant to an active investigation into whether President Trump’s campaign officials coordinated activities with the government of Russia, one of those officials lied to the F.B.I. about coordinating activities with the government of Russia,” Mr. Gleeson wrote. “It is hard to conceive of a more material false statement than this one.”

The government’s ostensible grounds for seeking dismissal are conclusively disproven by its own briefs filed earlier in this very proceeding,” Mr. Gleeson wrote. “They contradict and ignore this court’s prior orders, which constitute law of the case. They are riddled with inexplicable and elementary errors of law and fact. And they depart from positions that the government has taken in other cases.”

Mr. Flynn’s defense team and the Justice Department have sought to bypass Judge Sullivan altogether, asking the Court of Appeals for the District of Columbia Circuit to order him to dismiss the case against Mr. Flynn without any further review. The accused Judge Sullivan of abusing his power by appointing Mr. Gleeson to offer counterarguments.

In a filing last week in that proceeding, a lawyer for Judge Sullivan argued that he should be permitted to complete his review, and said he would not necessarily adopt the findings of Mr. Gleeson. A three-judge panel is scheduled to hear arguments in that request on Friday.

Mr. Flynn had pleaded guilty to lying to the F.B.I. in December 2017 about his conversations with the Russian ambassador the previous month, during the transition period after Mr. Trump won the 2016 election. The Obama administration was taking actions to punish Russia for its interference in the American democratic process, including imposing sanctions on Russian intelligence agencies and expelling Russian officials from the United States. Newly declassified transcripts showed that the sanctions were the main point of the conversations that Mr. Flynn lied about.

American officials intercepted those calls because they were wiretapping the Russian ambassador, Sergey I. Kislyak, and heard Mr. Flynn disparage the punishments and urge Moscow not to escalate the dispute — holding out the prospect of working together after Mr. Trump’s inauguration on issues like fighting the Islamic State. The ambassador later told Mr. Flynn that he had conveyed the “proposal” and that Russia’s government had decided to not retaliate as a result.

But when word of Mr. Flynn’s communications began to emerge, Mr. Flynn lied about what the two had discussed to several incoming members of the administration, including Vice President Mike Pence. F.B.I. agents working on the Russia investigation had previously decided to close an investigation into Mr. Flynn, having not found evidence he was a Russian agent, but decided to question him.

The Justice Department, in seeking to drop Mr. Flynn’s case, have portrayed that interview as baseless because the F.B.I. was moving to close the investigation into Mr. Flynn before the issue of the calls — and Mr. Flynn’s pattern of lying about them to his colleagues — arose. But Mr. Gleeson argued that the calls and lies gave the F.B.I. good reason to question Mr. Flynn.

“These developments added new dimensions, as well as newfound urgency, to the F.B.I.’s ongoing investigations and the intelligence community’s counterintelligence concerns,” Mr. Gleeson wrote. “Flynn had lied to multiple incoming White House officials and concealed the true nature of his contacts with the Russian government.”

Mr. Trump soon fired Mr. Flynn, citing his lies to other members of the administration about his calls with the ambassador, Mr. Flynn eventually twice pleaded guilty to a criminal charge of making false statements. His plea was part of a deal to cooperate with prosecutors, which also resolved Mr. Flynn’s liability for failing to register as a paid foreign agent of Turkey in 2016 and then signing forms where he lied about that work, another potential criminal charge.

But Mr. Flynn’s case became a political cause for Mr. Trump’s supporters as he attacked the legitimacy of the overall investigation that sought to understand Russia’s election interference and was eventually led by the special counsel, Robert S. Mueller III. And in January, after changing defense lawyers, Mr. Flynn sought to withdraw his guilty plea.

Although he had previously told the court that he did lie to the F.B.I. agents, he now said that he simply did not remember what he had spoken about with the Russian ambassador and that he did not lie.

After more than two years of asserting that Mr. Flynn’s lies were material to the F.B.I.’s Russian interference investigation, the Justice Department in a sharp reversal said they were not in its motion to drop the case.

“That is about as straightforward a case of materiality as a prosecutor, court, or jury will ever see,” Mr. Gleeson wrote.