It was not clear what the "top secret" emails were about, but it marks the first time that the State Department has made the acknowledgement.
The emails were deemed "top secret" at the request of intelligence officials, State Department Spokesperson John Kirby said, adding that they were not marked classified at the time they were sent. But, Kirby said, the State Department is now conducting a separate investigation into whether or not those emails should have been marked classified at the time. He did not know when that investigation would be complete.
Since late last year the FBI has also been conducting an investigation into whether or not classified information was improperly handled.
Clinton's campaign called for a release of the "top secret" emails in a statement Friday, claiming the emails have been overly classified and misrepresented.
"We firmly oppose the complete blocking of the release of these emails," campaign spokesman Brian Fallon said in the statement. "Since first providing her emails to the State Department more than one year ago, Hillary Clinton has urged that they be made available to the public. We feel no differently today."
Fallon has also accused the intelligence community of conspiring with congressional republicans to discredit Clinton's campaign for presidency. Republicans have denied that.
Meanwhile the department fell well short of a court-ordered mandate to release all 55,000 pages of the former Secretary of State's emails by today.
It was required as part of a Freedom of Information Act (FOIA) lawsuit to finish the production today and release the remaining 9,900 pages of her emails. But at 7 p.m. tonight it posted just under 1,700.