Republican legislators on Thursday launched a new bid to scrutinize Hillary Clinton for her use of a private email server while she was secretary of state, questioning the FBI director for nearly five hours about how — after a year-long investigation that found Clinton’s setup to be problematic — he came to believe the matter should be closed with no criminal charges.

The hearing before the House Oversight and Government Reform Committee previews what is likely to be a months-long effort to call the presumptive Democratic presidential nominee’s credibility and judgment into question. Meanwhile, the State Department announced that it was reopening its internal review into the matter — which could potentially bring professional consequences for Clinton or her top aides there.

On Capitol Hill, Republicans asked FBI Director James B. Comey repeatedly how Clinton’s public statements differed from his investigators’ findings; how Comey could consider Clinton “careless” but not criminal; and whether Clinton was being given a pass because of who she is.

“We’re mystified and confused by the fact pattern that you laid out and the conclusions that you reached,” the committee’s chairman, Rep. Jason Chaffetz (R-Utah), told Comey. “It seems that there are two standards, and there’s no consequence for these types of activities and dealing in a careless way with classified information. It seems to a lot of us that the Average Joe, the average American, that if they had done what you laid out in your statement, that they’d be in handcuffs.”

Attorney General Loretta E. Lynch is scheduled to appear Tuesday before the House Judiciary Committee, where she probably will face similar inquiries.

Even under the relentless questioning from House Republicans, Comey asserted unequivocally that it would have been unfair and virtually unprecedented to bring a criminal case against Clinton under current laws.

“As a non-lawyer, as a non-
investigator, it would appear to me you have got a hell of a case,” an exasperated Rep. Earl L. “Buddy” Carter (R-Ga.) told Comey.

“I’m telling you we don’t, and I hope people take the time to understand why,” Comey responded.

Clinton campaign spokesman Brian Fallon said in a statement that Comey’s testimony “clearly knocked down a number of false Republican talking points.”

“The Director’s explanations shut the door on any remaining conspiracy theories once and for all,” Fallon said. “While Republicans may try to keep this issue alive, this hearing proved those efforts will only backfire.”

Comey did potentially give Clinton’s political rivals some ammunition, conceding that there was “evidence of mishandling” classified information and that an FBI employee who did the same “would face consequences for this.” He also notably asserted he was “not going to comment on the existence or nonexistence of any other investigations” when asked whether investigators had looked at the Clinton Foundation.

Comey said that he believed Clinton was “extremely careless; I think she was negligent” but that investigators did not find evidence she intended to do wrong with her email setup.

Republicans argued that Clinton knew she was skirting the rules, and late in the hearing, Chaffetz pointed to a 2011 email in which Clinton told an aide to turn a fax “into nonpaper w no identifying heading and send nonsecure.” The aide had been having trouble getting the document in Clinton’s hands.

Comey said Clinton told FBI agents that she was intending to instruct the aide to “make it into a non-classified document.” He said he believed Clinton asked for the header to be removed because it would have no longer been necessary, if the document were no longer classified.

“You are very generous in your accepting of that,” Chaffetz responded.

Republicans also questioned aggressively how Comey could conclude that no charges should be brought if he felt Clinton was careless. In recent days, many have pointed to a section of the Espionage Act that allows for prosecutions of those who, through “gross negligence,” let classified information “be removed from its proper place of custody or delivered to anyone in violation of his trust, or to be lost, stolen, abstracted, or destroyed.”

Comey said investigators examined that charge for Clinton and her staffers but found that a prosecution would have been virtually unparalleled. Federal authorities had brought one such case in nearly a century, and the circumstances were drastically different.

“No reasonable prosecutor would bring the second case in 100 years based on gross negligence,” Comey said.

Lawyers said the case to which Comey was referring is likely that of James Smith, an FBI agent who was accused in 2003 of having a sexual relationship with an informant who was alleged to have been a Chinese spy. Smith ultimately pleaded guilty to a charge of making a false statement, not a count under the Espionage Act.

Congressional Republicans also probed Thursday whether the FBI was concerned with Clinton’s prior congressional testimony that no emails marked classified ever traversed her private system, given that Comey previously rebutted that claim. Comey clarified at the hearing that investigators found three such emails with the notation “(C)” — meaning confidential — contained within the text and said it was “possible she didn’t understand what a ‘C’ meant when she saw it in the body of an email like that.”

Chaffetz asked whether the FBI had specifically investigated Clinton’s previous statements, which were in his view false, to Congress. Comey said to open a criminal investigation, he would need a referral from Congress.

“You’ll have one; you’ll have one in the next few hours,” Chaffetz said.

While Comey confirmed that Clinton did not lie to bureau investigators, he said he was “not qualified to answer” whether she had lied to the public.

“I really don’t want to get in the business of trying to parse and judge her public statements,” he said.

The much-anticipated appearance came just a day after the Justice Department formally closed its probe and two days after Comey announced his controversial recommendation that Clinton not be charged. Republican legislators have been waging an aggressive campaign to solicit more information from Comey, and the FBI director said he welcomed the opportunity to ­explain his decision-making to the American public. That, he said, is why he decided to announce his recommendation not to charge Clinton on Tuesday without consulting anyone at the Justice Department first.

“What I decided to do was offer transparency to the American people about the whys of that, because I thought that was very, very important for their confidence in the system of justice,” Comey said.

Comey has said previously that investigators looked at other cases involving classified information and could not find one that would support charges in the Clinton matter. He specifically addressed on Thursday the bureau’s investigation of former CIA director David H. Petraeus, distinguishing it from the Clinton email probe in no uncertain terms. He said that Petraeus — unlike Clinton — lied to the FBI and that investigators found classified material in his desk.

“Clearly intentional conduct,” Comey said of Petraeus. “Knew what he was doing was a violation of the law.”

But Comey also said that if an FBI agent were found to have been careless with classified information, that could result in a loss of security clearance, suspension or even termination. He declined to say precisely what consequence he felt Clinton should face.

“One of my employees would not be prosecuted for this,” he said. “They would face consequences for this.”

Comey said investigators had found no evidence that Clinton’s private server had been hacked, although others with whom she corresponded had. He explicitly batted down claims by the Romanian hacker Marcel Lehel Lazar — whose cyber-mischief revealed that Hillary Clinton was using a private email address — that he had gotten into Clinton’s account.

“He admitted that was a lie,” Comey said.

Comey has been the public face of the Clinton investigation, even eclipsing his boss, Lynch. Late last week, Lynch announced that she would accept the recommendation of career prosecutors and FBI agents to assuage questions about the investigation’s integrity, concerns that were intensified after Lynch met privately with former president Bill Clinton aboard her plane in Phoenix. Lynch and the former president have asserted the meeting was a chance, social encounter at which no pending cases were discussed, and Lynch has said she planned to accept career employees’ recommendation even before it occurred.

On Wednesday, she announced in a brief statement that she was accepting the recommendation of Comey and others and closing the probe involving Clinton.

A previous version of this report said Comey testified that investigators found classified materials in the attic of former CIA director David H. Petraeus. Comey later corrected himself, saying the materials were found in a desk.