Former Secretary of State Hillary Clinton’s secret email account may have broken laws governing handling of classified information, but it’s unlikely a prosecutor could make the charges stick, FBI Director James B. Comey said Tuesday, ending his yearlong investigation into the Democratic presidential candidate.

Mrs. Clinton was “extremely careless” in handling top-secret information, enemy hackers may have breached her email server, and she and her attorneys likely deleted protected government records, the FBI concluded.

Mr. Comey said investigators found 110 email chains that had classified material at the time Mrs. Clinton sent or received them through her secret server, and seven of those included information deemed to be the highest-level “special access program” data.

Because there is no evidence Mrs. Clinton meant to leak the information, he said, there is no reason to prosecute her.

“Although there is evidence of potential violation of the statutes regarding the handling of classified information, our judgment is that no reasonable prosecutor would bring such a case,” he said in announcing his findings.

Hours later, Mrs. Clinton campaigned with President Obama in North Carolina. The president ignored the news of the FBI investigation and instead urged voters to carry on his legacy by electing Mrs. Clinton to succeed him.

Attorney General Loretta Lynch will make the final decision on whether to prosecute, but Republicans were stunned by Mr. Comey’s announcement. They said he laid out a compelling case against Mrs. Clinton, but then refused to follow through to the logical conclusion of recommending charges.

House Speaker Paul D. Ryan of Wisconsin said Mr. Comey’s decision “defies explanation,” and several other Republicans renewed their call for a special prosecutor to take over the case from Ms. Lynch.

Donald Trump, Mrs. Clinton’s likely Republican opponent in the presidential race, said Mr. Obama and his political allies had circled the wagons to protect Mrs. Clinton.

“Folks — the system is rigged,” the billionaire businessman said in a statement. “The normal punishment, in this case, would include losing authority to handle classified information, and that too disqualifies Hillary Clinton from being president. The final jury will be the American people, and they will issue the verdict on her corruption, incompetence, and bad judgment on November 8th.”

Mrs. Clinton has been under investigation for a year after the congressional probe into the 2012 terrorist attack in Benghazi, Libya, uncovered her secret email account, which she set up shortly after she became secretary of state in early 2009.

That account, which she maintained on a server at her home in New York, was kept secret from the State Department’s own open-records division, effectively shielding Mrs. Clinton’s emails from public view for more than six years. It also left secret information open to hacking by enemies, Mr. Comey confirmed.

After prodding by the Benghazi investigative committee, the State Department asked Mrs. Clinton in 2014 to return her messages. She did so, then issued a number of explanations for her behavior, saying she kept the account at her home because it was more convenient and insisted it didn’t pose a security risk.

She returned some 32,000 messages to the State Department, saying her attorneys carefully reviewed them to make sure she caught all emails that dealt with official business. She expunged 30,000 other messages that she said were purely personal and had no bearing on her government service.

Mr. Comey on Tuesday refuted each of those statements. He said her behavior did pose a security risk, her attorneys did not review each message but performed only key-word searches and looked at email headers, and the FBI found some official business messages Mrs. Clinton didn’t turn over at all.

He said government employees who behave recklessly with classified data can face administrative punishments or have their security clearances stripped, but added that it’s not the FBI’s job to decide. As for criminal charges, he said prosecutors would likely have to prove Mrs. Clinton intended to breach security or that her negligence leaked a massive amount of classified data.

“We do not see those things here,” he said.

Legal analysts debated whether Mrs. Clinton should be charged. Former New York Mayor Rudolph W. Giuliani, speaking on MSNBC, said Mr. Comey’s description of Mr. Clinton’s behavior as “extremely careless” is strikingly close to the classified information law’s “gross negligence” standard.

Mr. Ryan and fellow Republicans on Capitol Hill said Mr. Comey should release more information about his decision if he wants the public to believe it wasn’t a political call meant to protect Mrs. Clinton.

Sen. Chuck Grassley, Iowa Republican and Senate Judiciary Committee chairman, said Mr. Comey should release details of his investigation.

Some conservatives argued that Mrs. Clinton could still face legal jeopardy for perjury. They pointed to sworn statements her attorneys made to federal courts that she had turned over all of her work-related emails.

But her campaign declared the case over.

“As the secretary has long said, it was a mistake to use her personal email and she would not do it again,” spokesman Brian Fallon said in a statement. “We are glad this matter is now resolved.”

Mr. Comey’s investigation was a black eye not only for Mrs. Clinton, but also for the department she used to run. The FBI concluded the “security culture of the State Department … was generally lacking in the kind of care for classified information that is found elsewhere in the U.S. government.”

State Department spokesman John Kirby bristled at the charge, saying employees take their classified information duties “very, very seriously.” He said department staffers go through “training and indoctrination” to ensure they handle material correctly.

He declined to answer questions about why that indoctrination failed in the case of Mrs. Clinton and her top aides.

Mr. Kirby also declined to say whether the department would revoke the security clearances of some of Mrs. Clinton’s top aides for their own roles in handling classified material.

“Our policy’s not to discuss it, and I’m not going to change the policy here today,” he said.

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