Ex- FBI chief James the former director has pleaded not guilty to giving untrue testimony to US legislators and hindering a legislative process.
Mr Comey's lawyer submitted the response acting as his counsel in a US district court in Alexandria, Virginia on mid-week.
The defense lawyer declared he would attempt to have the case terminated for multiple factors including that his defendant, a detractor of former President Trump, was being targeted.
James Comey was charged just days after Trump pushed his chief prosecutor to move forward against him.
In court on Wednesday, Comey's lawyer Mr Fitzgerald informed the magistrate they intended to submit several legal requests to dismiss the proceedings before a court case, arguing the government's case was retaliatory and that a US attorney was wrongfully appointed to assume control of the case.
James Comey's case was originally overseen by a Virginia prosecutor, who left his position under influence from Trump after his examination into another opponent - New York Attorney General Letitia James - did not succeed to initiate prosecution.
The former director came across in optimistic frame of mind as he came into the courtroom on mid-week, chatting with his legal team and being lighthearted. He was joined by his wife, Mrs Failor and offspring his daughter, a US lawyer who the Trump administration terminated.
Upon hearing to the magistrate state his rights and the two counts against him in legal proceedings on Wednesday, the defendant was questioned if he understood the accusations.
"Absolutely your honour. Appreciate it," he told the court.
The former director was the head of the FBI from 2013-2017 and was terminated about four months into Donald Trump's initial presidency as commander-in-chief. At the period, Mr Comey was overseeing an examination into international campaign influence and whether there were any links between Moscow and Trump's campaign.
Throughout his leadership, the director sparked a negative reaction from Democrats when he stated just days before the national vote that he was examining political contender Clinton's use of a personal email system. Indictments against the candidate were not pursued, resulting in negative feedback from conservative politicians as well.
The federal government assert James Comey provided false information to the legislature during a Senate Judiciary Committee hearing in recent years when he was being interrogated about both the Clinton investigation as well as the Russia election probe. They allege he deceived the legislative body by saying he had not permitted a person at the Federal Bureau of Investigation to disclose to media organizations details about the government examinations.
Legal representatives also accuse Mr Comey of "improperly attempting to sway, hinder and impede" the committee by making false statements to it.
In a video James Comey published to his social media after he was charged, he stated he was innocent and accused Trump of acting like a "dictator".
"My family and I have known for considerable time that there are costs to challenging the former president," he stated. "We refuse to live on our kneeling."
"I have done nothing wrong," he continued. "Therefore proceed with a trial."
These allegations against Mr Comey surfaced after Trump posted on social media calling for his attorney general, Pam Bondi, prosecute the former director and additional individuals.
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