"In fact, many times an investigation may find no wrongdoing?" Stewart asked.
"That's one of the reasons we don't talk about it, so we don't smear people who don't end up charged with anything."
But Comey did acknowledge the ongoing probe Monday, the first time the FBI has said there is an open review of whether there was collusion between Russia and Trump's team to sway the election.
"In unusual circumstances, where it is in the public interest, it may be appropriate to do so," Comey said of making public the investigation.
He declined to answer questions about individual Trump campaign and White House officials and whether they were part of the probe. Committee Chairman Devin Nunes, R-Calif., said because of the "big gray cloud" this has placed over the administration, the FBI should complete the investigation as quickly as possible so it can focus on the job of running the government.
In other testimony, Comey said there was no factual basis to confirm Trump's previous tweets saying that President Barack Obama had "wiretapped" Trump Tower in New York City during the campaign. The White House has said Trump does not plan to withdraw that allegation and argued that wire taps could include several types of surveillance.
The FBI director said there was no wire taps and that a president cannot unilaterally order such a move.
"I have no information that supports those tweets," Comey said of Trump's charges.
Democrats during the more than five-hour hearing focused on Trump and his team's ties to Russia and that country's efforts to meddle with the presidential election. Comey said that intelligence points to the fact Russia was trying to undermine confidence in the election and to hurt Democratic nominee Hillary Clinton, but the agencies did not attempt to make a determination whether those efforts succeeded in swaying the election.
Stewart, and fellow Republicans, turned their attention many times to those government officials who have leaked information about Russia to the news media, with the Utah congressman calling the leakers "arrogant and cowards."
"I hope you find those guys and I hope you crack them on the head," Stewart said.
He also attempted to drill down on the intelligence agencies' assessment that the Russians had a clear preference for Trump in the election, suggesting this was an overreach and that the motive simply could have been to hurt Clinton, the expected election victor, not a "hail Mary" pass to boost Trump.
"If anyone in the world attempted to tell me they concluded Mr. Trump was going to win, I'd just say they're nuts," Stewart said. "Because there was no one in the world who thought that."
Comey responded that the motives to undermine Clinton or to boost Trump were "two closely related sides of the same coin." He then compared it to his hatred for the New England Patriots, saying that made him an instant supporter of whatever team was on the field playing against them.
Trump, in a series of early morning tweets, his preferred method of talking to Americans, said that the Democrats "made up and pushed the Russia story" as an excuse for running a bad campaign and losing. Trump won the Electoral College but lost the popular vote.
Trump also blasted those who have leaked information to the news media.
"The real story that Congress, the FBI and all others should be looking into is the leaking of classified information," he tweeted. "Must find leaker now!"
House Minority Whip Steny Hoyer, D-Md., said the testimony by the FBI and the NSA director, Adm. Michael Rogers, underscores the need for a bipartisan, independent investigative commission.
"The American people deserve answers, and Congress must demand a full accounting," Hoyer said. "It's also deeply concerning that Republicans focused on the false issue of leaks rather than asking serious questions about Russia's assault on our democracy. This further demonstrates that is past time to establish a bipartisan, independent commission to investigate Russia's interference in our election and possible coordination with the Trump campaign. Our national security and the foundations of our system are at stake."
Comey noted it was an extraordinary situation for him and the NSA director to speak about the investigation publicly, even as the two declined to discuss many specifics of the probe or Russia's tactics used in efforts to manipulate the election.
"Now we're going to close our mouths and do our work," Comey said.