BCFC/iStockBy ALEXANDER MALLIN, ABC News

(WASHINGTON) -- The federal judge overseeing the case against former national security adviser Michael Flynn has signaled he's not quite ready to accept the Justice Department's surprise motion last week to throw out the charges.

In orders on Tuesday and Wednesday, U.S. District Judge Emmet Sullivan said he would be making way for outside interested parties, such as legal scholars or even former prosecutors involved in the case, to weigh in with 'friend of the court' briefs.

The order followed the Justice Department's move last Thursday to throw out the charges against Flynn, who had previously pleaded guilty twice for lying to FBI agents about his contacts with the former Russian ambassador during a January 2017 interview at the White House.

Attorney General William Barr, who said he was acting on a recommendation from a U.S. attorney he tasked with reviewing the Flynn case, argued that newly uncovered evidence about how the FBI agents had handled their investigation had since rendered the case illegitimate.

But the highly unusual intervention in a case against one of the president's top political allies drew outrage among many of Barr's critics, including more than 2000 former DOJ officials who called for his resignation in a public letter Monday.

A former DOJ official previously involved in the Flynn investigation who was repeatedly cited in the DOJ's filing also publicly accused Attorney General Barr of 'twisting' her words in order to paint a misleading narrative.

Sullivan's latest order could make room for such groups and individuals with an interest in the case to argue against the Justice Department's motion to toss the charges.

"Obviously the Justice Department's position is pretty clear in its filing," DOJ spokesperson Kerri Kupec said in response to Sullivan's order Tuesday during an interview with Fox News. "We do not believe this case should have been brought, we are correcting that and we certainly hope that in the interest of true justice the judge ultimately agrees and drops the case against Gen. Flynn."

Flynn's attorneys on Tuesday filed a motion seeking to block a group of former Watergate prosecutors from filing a brief in the case, arguing they had no relevance to the case. Judge Sullivan on Wednesday initially rejected the filing from the Watergate prosecutors, saying he still had yet to outline a schedule and process for accepting such briefs.

Legal experts who spoke to ABC News said that if Sullivan declines to accept DOJ's reasoning for throwing out the charges against Flynn he could still technically move forward with sentencing the former national security adviser, though such a decision would almost certainly face immediate appeal.

Separately, former judges said that if Sullivan has suspicions about the DOJ's motives he could seek to appoint an independent counsel to review the circumstances surrounding their reversal.

When overseeing the Justice Department's failed corruption case against former U.S. Sen. Ted Stevens in 2008, Sullivan appointed a group of independent lawyers to investigate the conduct of federal prosecutors after it was revealed they had failed to hand over exculpatory evidence and misled the jury.

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