The finding is likely to complicate Clinton’s efforts to move past the controversy, which has dragged down her poll ratings in her bid for the Democratic presidential nomination. And it comes as her potential Republican rivals have called for Clinton to be prosecuted for what they say was her mishandling of national secrets.

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In responding Friday, Clinton’s campaign took the unusual step of criticizing the intelligence community, accusing spy agencies of engaging in “overclassification run amok.” Some Clinton allies suggested that intelligence officials were politically motivated.

Clinton’s spokesman, Brian Fallon, presented the findings as the latest turn in an ongoing struggle between government officials over whether to retroactively classify emails that were not marked as sensitive when they were sent and that Clinton thinks should be made public.

“After a process that has been dominated by bureaucratic infighting that has too often played out in public view, the loudest and leakiest participants in this interagency dispute have now prevailed in blocking any release of these emails,” Fallon said. “This flies in the face of the fact that these emails were unmarked at the time they were sent, and have been called ‘innocuous’ by certain intelligence officials.”

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Fallon told MSNBC that withholding the emails from view in their entirety made it impossible for the public to independently judge the validity of the State Department’s conclusion.

Friday’s announcement came at a politically sensitive moment for Clinton. She is locked in a dead heat in Iowa with Sen. Bernie Sanders of Vermont, whose long-shot bid for the Democratic nomination has gained momentum in recent weeks, and the revival of the email matter could increase anxiety among Clinton supporters who had hoped that the issue would fade as the primaries began and a general election loomed.

Some uncertainty has hung over Clinton and her campaign since the revelation last spring that she had used a private email system for official business, with the FBI conducting an investigation into whether classified information was compromised.

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A U.S. law enforcement official familiar with the investigation said that prosecuting anyone involved in the case would be difficult. The official, who spoke on the condition of anonymity to discuss sensitive internal deliberations, said that investigators are looking at whether anyone knowingly mishandled classified information on the system.

The inquiry has frustrated Clinton allies and provided fodder to GOP candidates such as Sen. Marco Rubio of Florida, who mused in Thursday night’s Republican debate that Clinton was “disqualified from being the commander in chief” because she stored classified material on her server and “her first acts as president may very well be to pardon herself.”

Republicans were quick to chime in, with Donald Trump tweeting that it was a “disaster” for Clinton and asking, “How can someone with such bad judgement be our next president?”

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Sanders appeared to dismiss the email issue in October, when he told Clinton at a debate that Americans were “sick and tired of hearing about your damn emails.”

“As I said at the first Democratic debate, there is a legal process in place which should proceed and not be politicized. The voters of Iowa and this nation deserve a serious discussion of the issues facing them,” Sanders said Friday in a statement.

The Friday announcement was significant because it appeared to undercut Clinton’s argument in recent months that she was merely the victim of a bureaucratic squabble between overly strict analysts at the intelligence agencies and more reasonable reviewers at the State Department.

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The intelligence community’s inspector general had previously indicated that he thought that some of the emails contained top secret material. Until Friday, however, the State Department had declined to concur with that assessment.

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State’s reviewers had said that more than 1,300 Clinton emails contained classified material, but the vast majority were just “confidential,” a lower level of sensitivity.

Clinton has said that none of her emails were marked classified when they were sent. But it is the responsibility of individual government officials to handle classified material appropriately, including by properly marking it as classified, according to experts.

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Clinton has also said that the information in question was not classified at the time the emails were sent — a point that intelligence officials have disputed.

State Department spokesman John Kirby said Friday that his agency had not yet made a determination on that key question.

Kirby also said for the first time that some emails between Clinton and President Obama have been located and will also be withheld from public release. He said there were 18 emails between the two, comprising eight email chains. He said those emails were not classified but would take longer to be released, which is standard for presidential communication.

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Clinton’s position was supported Friday by Sen. Dianne Feinstein of California, the ranking Democrat on the Senate Intelligence Committee, who said none of the emails in question originated with Clinton.

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“It has never made sense to me that Secretary Clinton can be held responsible for email exchanges that originated with someone else,” she said in a statement. “The only reason to hold Secretary Clinton responsible for emails that didn’t originate with her is for political points, and that’s what we’ve seen over the past several months.”

Another Clinton ally, Agriculture Secretary Tom Vilsack, told MSNBC that Friday’s announcement suggested an effort to hurt Clinton ahead of Monday’s voting in Iowa.

“The timing of it is quite suspect,” said Vilsack, a former Iowa governor.

Steven Aftergood, who heads a project on government secrecy for the Federation of American Scientists, said he thought the attention to Clinton’s emails was overblown, partly because similar classification disputes are common across government.

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Still, he called Clinton’s public squabble with the intelligence community unusual.

“I think this is a unique set of circumstances in which a presidential candidate is engaged in a debate with an intelligence agency over her own record as a former official,” he said.

The State Department’s conclusion came as it has worked to process 55,000 pages of Clinton’s correspondence for public release, including about 1,000 pages that were released Friday night. Clinton has said that she deleted 31,000 additional emails in 2014, deeming them purely personal.

The State Department has been under a court order to release the documents in batches, once a month, as part of a lawsuit filed by reporter Jason Leopold of Vice News, who sued after the department failed to respond promptly to his request for the public documents.

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A judge had ordered the department to release all of the emails by the end of January, but attorneys for the department said this week that they would miss the deadline, and requested another month.

That means the last of Clinton’s emails will not be released until the end of February — after the Iowa caucuses and the New Hampshire primary — and just before Super Tuesday, when voters in 11 states will cast ballots.

Clinton, who held three campaign events across Iowa on Friday, has encouraged the State Department to release her email as quickly as possible.

“I think it’s great. Let people sort them through,” Clinton said at a town hall sponsored by CNN in Iowa this week. “And as we have seen there is a lot . . . [of] interest. But it’s something that took time to get done.”

Although in September she said her decision to use the private account was a mistake, at the town hall this week she said she did not believe it amounted to “an error in judgment.”