Twenty-two emails sent through Hillary Clinton's unsecured home server while she was secretary of state contained government secrets, US officials say.
The State Department said the messages were "top secret" and could not be released.
Spokesman John Kirby said the emails were not marked classified at the time they were sent.
Mrs Clinton's use of a personal email as secretary of state has dogged her bid for the US presidency.
Mrs Clinton, who is seeking the Democratic nomination for the 2016 election, has been under fire for using a private computer server for work emails while in office.
On her request, thousands of those emails have been released by the State Department.
But this is the first time her messages have been labelled classified at any level.
Her campaign reacted angrily to the announcement, demanding that the emails be released in full.
"This appears to be over-classification run amok," it said in statement.
It comes three days before she competes in the Iowa presidential caucuses – the first time the public will cast their votes in the run-up to November's election.
Messages were marked "top secret" because they would cause "exceptionally grave" damage to national security if disclosed, the State Department said.
Intelligence officials told the Associated Press that the 37 pages being withheld concerned so-called "special access programmes" – clandestine projects such as drone strikes or government eavesdropping.
It was unclear whether Mrs Clinton sent "top secret" messages or only received the information.
Previously, sensitive information has been redacted from the published messages, but Mr Kirby said the "top secret" emails would not be released, even in part.
Mrs Clinton's opponents have accused her of putting US security at risk by using an unsecured computer system.
The presidential hopeful has admitted that her decision to use a private email server at her New York home was a mistake.
The State Department released another batch of Mrs Clinton's emails on Friday evening.
The department has yet to release about 7,000 pages of emails from her private server.
Officials in the State Department have asked for additional time to vet the messages because of the recent snowstorm that hit Washington.
They have asked to release the final batch messages on 29 February, which is after the Iowa caucuses and the New Hampshire primary.
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