The presidential hopeful has insisted she never sent sensitive information on her private account
The US State Department says 22 emails on Hillary Clinton's private server are marked top secret.
Seven email chains, 37 pages, are being withheld in full for containing material representing the highest level of classification.
Eighteen of the emails were between the former Secretary of State and President Barack Obama, according to CBS News.
But the State Department has said it is not clear whether the emails were classified at the time they were sent.
Friday's announcement is the first time the Obama administration has confirmed Mrs Clinton's unsecured home server contained some closely guarded secrets.
The revelation comes just three days before Mrs Clinton faces the first White House nominating vote, in the Midwestern state of Iowa, ahead of November's presidential election.
The State Department will release more emails on Friday from Mrs Clinton's time as America's top diplomat, the latest tranche of some 55,000 of her messages the agency has been reviewing.
After it emerged she had been using a private email last year, Mrs Clinton 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 when New Jersey Governor Chris Christie accused Mrs Clinton of putting "American intelligence officers at risk".