According to the State Department, 22 emails sent through Hillary Clinton’s unsecured home server while she was secretary of state contained government secrets.
The messages were “top secret” and could not be released, the State Department adds.
Spokesman John Kirby said the emails were not marked classified at the time they were sent.
Hillary Clinton’s use of a personal email as secretary of state has dogged her bid for the US presidency.
The former first lady, 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 Hillary Clinton’s request, thousands of those emails have been released by the State Department, but this is the first time her messages have been labeled 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 Hillary Clinton 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 programs” – clandestine projects such as drone strikes or government eavesdropping.
It was unclear whether Hillary Clinton sent “top secret” messages or only received the information.
Previously, sensitive information has been redacted from the published messages, but John Kirby said the “top secret” emails would not be released, even in part.
Hillary Clinton’s opponents have accused her of putting US security at risk by using an unsecured computer system.
She 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 Hilalry Clinton’s emails on January 29.
The department has yet to release about 7,000 pages of emails from Hillary Clinton’s 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 February 29, which is after the Iowa caucuses and the New Hampshire primary.
Former Secretary of State Hillary Clinton has responded to a growing controversy over using her private email account for government business.
Hillary Clinton urged officials to release those emails, tweeting: “I want the public to see my email.”
This came after her emails were subpoenaed by a congressional committee investigating the deadly attack on the US embassy in Benghazi in 2012.
The state department is examining Hillary Clinton’s use of a personal email account as a possible breach of federal law.
The controversy has put Hillary Clinton under pressure as she is widely believed to be planning a bid for the Democratic presidential nomination in 2016.
In the tweet, Hillary Clinton wrote: “I asked State to release them [emails]. They said they will review them for release as soon as possible.”
It was revealed on March 4 that Hillary Clinton had her own internet server at her home in New York.
As the secretary of state in 2009-2013, Hillary Clinton did not have a government email address, the US state department told The New York Times.
Government watchdogs and former officials from the National Archives and Records Administration told the newspaper that Hillary Clinton’s use of private email alone, without any government account, was a serious breach.
Others cited concerns that a personal email account could be vulnerable to hackers.
The matter has been complicated by Associated Press reports that an internet server was registered under the name of Eric Hoteham at Hillary Clinton’s home in Chappaqua, New York.
The correspondence of federal officials is considered government records under federal law and Hillary Clinton has already had to hand over 55,000 pages of emails to the State Department.
On March 3, Nick Merrill, a spokesman for Hillary Clinton, declined to say why she used a personal account at the state department, but defended its use.
Hillary Clinton had complied with the “letter and spirit of the rules”, Nick Merrill said.
Her tweeted statement came just hours after the Republican-led congressional committee had demanded that Hillary Clinton turn over all emails relating to the Benghazi attack in which US ambassador Christopher Stevens was killed.
The chairman of the Benghazi committee, Trey Gowdy, told reporters: “I want the documents. Sooner rather than later.”
Democrats on the committee have criticized the decision arguing it is a politically-motivated hunt by Republicans.
“Everything I’ve seen so far has led me to believe that this is an effort to go after Hillary Clinton, period,” said Elijah Cummings.