Comey, who appeared under subpoena, announced after the meeting that he would return for more questioning Dec. 17. Appearing annoyed, he said "we're talking about Hillary Clinton's emails, for heaven's sake, so I'm not sure we needed to do this at all."
A transcript of the interview, expected to be released shortly, "will bore you," Comey said.
Two GOP-led committees brought Comey in as they sought to wrap up a yearlong investigation into the department's decisions in 2016. Republicans argue that department officials were biased against Donald Trump as they started an investigation into his campaign's ties to Russia and cleared Democrat Hillary Clinton in the probe into her email use. Comey was in charge of both investigations.
Democrats have said the investigations by the House Judiciary and Oversight and Government Reform committees are merely a way to distract from and undermine special counsel Robert Mueller's Russia probe. Mueller took over the department's investigation when he was appointed in May 2017.
After the questioning was underway, some Republicans signaled they were unhappy with Comey's level of cooperation. California Rep. Darrell Issa said Comey had two lawyers in the room, his personal lawyer and a lawyer from the Justice Department. He said the department lawyer repeatedly instructed Comey not to answer "a great many questions that are clearly items at the core of our investigation."
Democrats disagreed.
"He answered the questions he had to answer," said Rep. Raja Krishnamoorthi of Illinois. But he added that he was left with the impression that "we got nowhere today."
Florida Rep. Ted Deutsch said the Republican majority "wishes to only ask questions still about Hillary Clinton's emails, all to distract from the big news today, which is what's happening in court."
As the interview with Comey ended, Mueller revealed new details about his Russia investigation in court on Friday in the cases of Trump's former campaign chairman, Paul Manafort, and former personal lawyer Michael Cohen.
It was unclear if Comey is returning the week after next because Republicans felt he was being uncooperative, or if it was an issue with timing. While such closed-door interviews often extend late into the night, lawmakers said Friday that the interview would end in the afternoon because of scheduling issues.
Just as the meeting ended, President Trump tweeted that "it is being reported that Leakin' James Comey was told by Department of Justice attorneys not to answer the most important questions. Total bias and corruption at the highest levels of previous Administration. Force him to answer the questions under oath!"
While it was uncertain if Comey spoke under oath Friday, lying to Congress is a crime under any circumstance.
Over the past year, Republicans on the two committees have called in a series of officials and suggested after the closed-door meetings that there is evidence of bias at the Justice Department. The investigation's most public day was a 10-hour hearing in which former FBI special agent Peter Strzok defended anti-Trump texts he sent to a colleague as he helped lead both investigations. Strzok fought with Republican lawmakers in a riveting hearing that featured Strzok reading aloud from his sometimes-lewd texts, and Democrats and Republicans openly yelling at each other.
New York Rep. Jerrold Nadler, the top Democrat on the Judiciary panel, vowed to end the investigation when Democrats take the House majority in January.
"This is a waste of time to start with," Nadler said. "The entire purpose of this investigation is to cast aspersions on the real investigation, which is Mueller. There is no evidence whatsoever of bias at the FBI or any of this other nonsense."
Nadler and the top Democrat on the Oversight panel, Maryland Rep. Elijah Cummings, said in a statement after the meeting that Comey's testimony yielded few new details.
"As the special counsel's investigation appears to be closing in on the president and his associates, our Republican colleagues seem intent on spending their final days in power attempting to provide cover to President Trump and attempting to re-litigate the Department of Justice's decision not to prosecute Secretary Clinton," the Democrats said.
Comey, who has testified publicly on Capitol Hill about both the Clinton and Russia investigations, appeared for the interview after unsuccessfully fighting the subpoena in court. It was the first time he answered lawmakers' questions since an explosive June 2017 hearing in which he asserted that Trump fired him to interfere with his FBI investigation of alleged Russia ties to the Trump campaign.
His lawyers said he would prefer to testify publicly and said the committees were prone to selectively reveal information for political purposes.
"Don't do it in a dark corner and don't do it in a way where all you do is leak information," said Comey's attorney, David Kelley.
Under the deal struck with the Judiciary Committee, Comey was to be free to speak about Friday's questioning and a transcript was to be released soon afterward.
A report released this June from the Justice Department's internal watchdog said Comey was "insubordinate" in his handling of the Clinton email investigation in the final months of the 2016 campaign. But it also found there was no evidence that Comey's or the department's final conclusions were motivated by political bias toward either candidate.
The report said the former FBI director, who announced in July 2016 that Clinton had been "extremely careless" with classified material but would not be charged with any crime, repeatedly departed from normal Justice Department protocol. Yet it did not second-guess his conclusion that Clinton should not have been prosecuted, despite assertions by Trump and his supporters that anyone less politically connected would have been charged.