WASHINGTON — A lawyer hired by the federal judge overseeing the case of former Trump national security adviser Michael Flynn urged a federal appeals court Monday not to force him to end it now.

But in a separate court filing, the Justice Department said the case should be ended because only prosecutors, not judges, can decide when to abandon a criminal case.

The government last month told Federal District Court Judge Emmet Sullivan it wanted to drop the case, after Attorney General Williams Barr decided that Flynn’s false statements to the FBI were not material to any open investigation. Sullivan appointed a former judge to argue the opposite point so that he could have a hearing on whether dropping the case would be in the public interest.

Flynn asked the federal appeals court in Washington to order Sullivan to grant the government’s motion and drop the case. But Beth Wilkinson, a former Justice Department lawyer appointed to represent Judge Sullivan, said the appeals court should give the judge a chance to rule first.

“If Judge Sullivan’s decision is anything short of what the parties sought, this court will have a chance to review it, without writing on a blank slate,” she said. “There is no reason for this court to enter the fray now.”

After pleading guilty twice, Flynn reversed course and said he didn’t lie to the FBI about his conversations with Russia’s ambassador to the US. But Wilkinson asked, what about Flynn’s separate false statements in which he denied that he did lobbying work for Turkey? They were part of his plea agreement.

And she said the judge wanted to examine the fact that the career prosecutors who worked on the Flynn case did not sign off on the motion to drop the charges, a fact that she called unusual.

Sullivan appointed retired judge John Gleeson to serve as a friend of the court and instructed him to argue against the department’s request, including whether to hold Flynn in contempt for perjury for changing his story about whether he lied to the FBI. Sullivan “will not blindly accept Gleeson’s recommendations,” Wilkinson said.

Flynn asked the appeals court to order Sullivan to shut the case down, arguing that a decision about whether to pursue a prosecution is entirely in the hands of the Justice Department, not the judge.

Once the government seeks to abandon a prosecution, his lawyers said, the judge has virtually no choice but to accept that decision and “has no authority to adopt the role of the prosecutor.” Sullivan’s efforts to appoint Gleeson as a friend of court shows “a disturbing lack of appreciation of the court’s limited role.”

In its filing Monday, the Justice Department said it has “exclusive and absolute discretion to decide whether to prosecute a case” and that the judge must assume that prosecutors have done their duty properly unless there’s clear evidence to suggest otherwise.

The government’s brief also defended the decision to drop the case and questioning the FBI’s actions in pursuing the charges in the first place.