Fox News contributor and Washington Examiner chief political correspondent Byron York told "The Story" Wednesday that retired federal judge John Gleeson's recommendation to U.S. District Judge Emmet Sullivan that he reject the Department of Justice's request to dismiss the case against Michael Flynn misses the key point.

"There is a lot that the Justice Department could disagree with in factual terms," York said, "but there is also that bigger issue, which is the ... the executive branch has the right to do this, not the judge."

COURT APPOINTED ATTORNEY SAYS JUDGE SHOULD BLOCK DOJ MOVE TO DROP FLYNN CASE

Gleeson, who was appointed by Sullivan last month to submit a brief discussing whether federal prosecutors should be able to dismiss the case against Flynn, insisted in a filing Wednesday that not only does Sullivan have the authority to reject the government’s request but he should do so.

The Federal Rules of Criminal Procedure state that prosecutors may dismiss a case “with leave of court.” At issue in the Flynn case now is exactly what level of discretion this gives the court.

"It is not the judge's responsibility to charge Michael Flynn [with perjury] or deny the Justice Department's right to do that," York insisted.

In an interview with Fox News’ Bret Baier earlier this week, Attorney General Bill Barr claimed that Sullivan was encroaching on the Justice Department’s authority.

“The argument is that it's always been understood that decisions whether to pursue an individual through the prosecution process or holding them criminally accountable is vested in the executive branch and not the courts,” Barr said. “And he is essentially, in our view, trying to set himself up as an alternative prosecutor.”

Fox News' Ronn Blitzer, and Bill Mears contributed to this report.