Those 37 pages, contained within seven email chains dating back to Clinton's tenure as US Secretary of State, will be withheld from a batch scheduled to be released later Friday.
"The documents are being upgraded at the request of the intelligence community, because they contain a category of top secret information," State Department spokesman John Kirby said.
Kirby clarified that the messages had not previously been designated as top secret, although the department "is focusing on whether they need to be classified today."
Clinton's use of her personal email address for official business as Secretary of State from 2009 to 2013 has become an ongoing scandal that some Republican opponents have used to attack her. Clinton, meanwhile, has long maintained that she did not send or receive information that, at the time, could have been considered classified.
Clinton and Senator Bernie Sanders are in a tight race in Iowa, which holds caucuses on Monday that start the 2016 primary calendar.
After the department's announcement, Clinton press secretary Brian Fallon said in a statement that the campaign objected to the decision to withhold the seven email chains and sought full transparency.
"We firmly oppose the complete blocking of the release of these emails," Fallon said. "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."
He said the documents originated in the State Department's unclassified system before they ever reached Clinton, and "in at least one case, the emails appear to involve information from a published news article."
"This appears to be overclassification run amok," Fallon said.
Clinton's use of a home email server was not expressly forbidden or illegal, but she acknowledged that the decision was probably a mistake.
The State Department has been releasing monthly batches of the emails following a court order last summer.