Seven email chains, covering 37 pages, are being withheld in full for containing material representing the highest level of classification.
State Department spokesman John Kirby said the messages were not classified at the time they were sent, but would not say whether Mrs Clinton sent them herself.
The agency refused to discuss the substance of the correspondence.
But the Associated Press reports some of the emails could be linked to secret sources, drone strikes or government eavesdropping.
The revelation comes just three days before Mrs Clinton faces the Iowa caucuses, when the first votes are cast for the Democratic and Republican presidential nominees.
Her campaign reacted with dismay to the State Department announcement, blaming it on "over-classification run amok" and "bureaucratic infighting".
"We firmly oppose the complete blocking of the release of these emails," its statement said.
It is the first time the Obama administration has confirmed Mrs Clinton's unsecured home server contained some closely guarded secrets.
The State Department is releasing more emails on Friday from her time as America's top diplomat between 2009-13.
But a further 18 messages, from eight email chains, between the former Secretary of State and President Barack Obama will not be published.
The State Department said those emails have not been marked classified and they may be released after President Obama leaves office next year.
It is the latest tranche of some 55,000 of her messages the agency has been reviewing.
More than 1,000 messages have been previously marked at lower classification levels for public release.
The FBI also is looking into Mrs Clinton's email setup but has said nothing about the nature of its inquiry.
Mrs Clinton, the front-runner to become the Democratic Party's White House nominee for November's election, has maintained her use of a private account broke no regulations.
After it emerged in March last year that she had been using a private email, she conceded it would have been "smarter" to use a government address.
But she insisted she never sent sensitive information through the account.
The US government forbids transmitting classified information outside secure, government-controlled networks.
The email affair came up in Thursday night's Republican presidential debate.
New Jersey Governor Chris Christie accused Mrs Clinton of putting "American intelligence officers at risk".
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