After repeated questioning by US District Judge Michael Nachmanoff, prosecutors acknowledged that the final version of the indictment was never presented to the entire grand jury that approved the charges after panel members previously rejected one of the proposed criminal counts.
Lawyers for Comey, one of three prominent critics of the Republican president indicted by Trump's Justice Department in recent months, used a 90-minute hearing in Alexandria, Virginia, to argue for throwing out the indictment ahead of the trial, currently scheduled for January.
Defence lawyer Michael Dreeben told Nachmanoff the procedural error acknowledged by the prosecution regarding the indictment was yet another reason for dismissal. Comey pleaded not guilty after being charged in September with making false statements and obstructing a congressional investigation.
A ruling by Nachmanoff to dismiss the case would be a major embarrassment for Trump's administration and would highlight a growing wave of scepticism within the judiciary about his efforts to prosecute political enemies.
The hearing focused on Comey's argument that he is the target of an improper "vindictive" prosecution brought solely to punish him for his criticism of the president, who fired him in 2017 amid an FBI investigation into contacts between Trump's 2016 election campaign and Russians.
Dreeben during the hearing called the case "a blatant use of criminal justice to achieve political ends."
The actions of Lindsey Halligan, the Trump ally serving as US Attorney for the Eastern District of Virginia, were in the spotlight during the hearing.
In a tense but brief exchange, Nachmanoff posed questions directly to Halligan asking her to explain what version of the indictment was presented to the grand jury and who was present.
Prosecutors in a Wednesday evening court filing sought to downplay the significance of the technical dispute over the Justice Department's handling of the indictment, arguing that it was not grounds for dismissing Comey's case.
The filing said the proposed indictment that was shown to the grand jury contained three criminal counts, two of which the panel approved.
After the panel declined to indict Comey on one of the charges, prosecutors dropped that count from the indictment, but did not change the language of the other charges when they prepared a subsequent two-count indictment, it said. That version was signed by the jury foreperson but not seen by the full grand jury, prosecutors wrote in their filing.
The prosecution has accused Comey of lying to a Senate committee when he said he stood behind prior testimony denying that he authorised disclosures about FBI investigations to the news media.
Comey has launched a multi-pronged effort to have the charges dismissed before a trial.Â
His lawyers pointed to Trump's years of social media broadsides against Comey dating to his firing in 2017. Comey later called Trump unfit for office.
