Hillary Clinton wasn’t “sophisticated enough” to know she was risking national security when she sent and received classified information, so it was impossible to make a criminal case against her, FBI Director James B. Comey told Congress on Thursday.

He said Mrs. Clinton, the former State Department secretary and now the presumptive Democratic presidential nominee, was briefed on the State Department’s policies but broke them, sending or receiving more than 100 messages that contained information that was confidential at the time she handled it. He also confirmed that she misled voters in her public explanations, and he insisted that she would have faced discipline, including potentially losing her right to see secret information, if she were still a government employee.

But he said his investigators couldn’t find any evidence that Mrs. Clinton intended to break the law, which he said means they couldn’t recommend that she be prosecuted.

“Certainly, she should have known not to send classified information,” Mr. Comey told the House Oversight and Government Reform Committee. “I think she was extremely careless. I think she was negligent. That, I could establish. What we can’t establish is that she acted with the necessary criminal intent.”

In five hours of testimony, Mr. Comey painted a picture of Mrs. Clinton as out of her depth when it came to understanding technology and not altogether aware of the classified information swirling around her. But Mr. Comey said her lapses came out of ignorance, not out of an effort to share secret information with the country’s enemies.

He also said the Justice Department believes the law imposing penalties for mishandling classified information, which does not on its face require criminal intent, may be unconstitutional.

The director said that making an example out of Mrs. Clinton would have been “celebrity hunting,” and that would have been unfair to her. “I know that frustrates people, but that’s the way the law is. That’s the practice in the Department of Justice,” he said.

Republicans said that by not making an example of Mrs. Clinton, Mr. Comey set a precedent that carelessness — including letting others without clearance see top-secret information — is an excuse, particularly if it involves a high-profile political figure.

“The average American, if they’d done what you laid out, they’d be in handcuffs,” said Rep. Jason Chaffetz, Utah Republican and oversight committee chairman.

Mr. Comey closed his yearlong investigation this week by concluding that Mrs. Clinton may have broken the law and was “extremely careless,” but he said he and all of his top investigators thought she shouldn’t be charged. On Wednesday, Attorney General Loretta E. Lynch agreed by announcing she was closing the case against Mrs. Clinton and her top aides.

Late Thursday, the State Department said it was kick-starting its own investigation into the handling of classified information during Mrs. Clinton’s four years as secretary. The department said it postponed its own investigation to give space to the FBI’s criminal probe.

The renewed probe has no deadline but could result in sanctions, including loss of security clearances for Mrs. Clinton and some of her top aides.

Mrs. Clinton used a secret server she kept in the basement of her New York home to conduct official business. She said publicly that she didn’t send or receive classified information, that she complied with department policies and that she returned all of the work-related messages to the government in December 2014.

Mr. Comey refuted each of those explanations.

“We found work-related emails, thousands, that were not returned,” he said.

He said he could find no evidence that Mrs. Clinton lied to his investigators but didn’t look into whether she lied to Congress. Mr. Chaffetz said he would quickly issue a criminal referral asking Mr. Comey to pursue that line of questioning.

Under questioning, Mr. Comey declined to say whether he was investigating activities of the Clinton Foundation, suggesting more political jeopardy for the presumptive Democratic presidential nominee.

The FBI director did dismiss some of the more pointed Republican speculation about Mrs. Clinton’s behavior, including that the hacker “Guccifer” gained access to her system. Mr. Comey said the FBI interviewed Guccifer and he admitted he had lied.

Mr. Comey also said there is no concrete evidence that enemy countries gained access to her system, though there is evidence that foreign governments tried. He said it’s impossible to know whether they did gain access, given the nature of Mrs. Clinton’s system.

Mr. Comey vehemently disputed conservatives’ speculation that his investigation was tarnished. He said he faced no political interference from the White House, the Clinton campaign or anyone else, and that the timing of his announcement was entirely his choice.

Although Mrs. Clinton sent and received dozens of messages that contained classified information, much of the hearing focused on three messages that contained markings — a “(C)” next to some paragraphs — which under State Department practice meant the information that followed was to be treated as classified.

Before he began the investigation, Mr. Comey said, he assumed everyone with access to high levels of classified information would have known the importance of the (C) marking. But he said after talking with Mrs. Clinton, he was no longer sure “whether she was actually sophisticated enough to understand what a C in parentheses means.”

“It’s possible — possible — that she didn’t understand what a C meant when she saw it in the body of an email like that,” he said.

Democrats said the (C) was a “tiny, little” marking that Mrs. Clinton could easily have missed — something Mr. Comey said was indeed possible. The State Department said those messages probably shouldn’t have been marked classified anyway.

“Those markings were a human error. They didn’t need to be there,” department spokesman John Kirby told reporters Wednesday.

Documents with secret information are supposed to be marked with a header saying they are classified, and none of the three emails with the (C) markings had that header information, Mr. Comey said. That meant they were not properly marked according to the rules, he said.

Brian Fallon, a spokesman for Mrs. Clinton’s campaign, said the hearing did little damage other than to show his boss was technologically incompetent.

“Director Comey’s testimony clearly knocked down a number of false Republican talking points and reconciled apparent contradictions between his previous remarks and Hillary Clinton’s public statements,” he said in a statement.

But Republicans said Mr. Comey left plenty of room for questions about Mrs. Clinton’s behavior and about his own conclusion that there wasn’t enough evidence to prosecute.

“Before I came to Congress, I spent several years as a criminal court judge. I presided over several hundred felony criminal cases. And I can assure you that I saw many cases where the evidence of criminal intent was flimsier than the evidence in this case,” said Rep. John J. Duncan Jr., Tennessee Republican.

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