The state department will be denying in full seven email chains found in 22 documents, representing 37 pages.
"These documents were not marked classified at the time they were sent," the state department Spokesman John Kirby said.
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"The documents are being upgraded at the request of the intelligence community because they contain a category of top secret information," Kirby said.
"We have worked closely with our inter-agency partners on this matter, and this dialogue with the inter-agency is exactly how the process is supposed to work," he said.
Further, Kirby said another 18 emails which comprised eight distinct email chains between Clinton and US President Barack Obama, are also being withheld in full from the state department's release of documents.
"The decision to withhold presidential correspondence from State's Freedom of Information Act production of former Secretary Clinton's emails was widely covered months ago," he said.
"They are entirely separate and distinct from the emails in today's release that were upgraded to top secret, secret, or confidential, and I'm not going to speak again to the content of that email traffic," Kirby said.
The announcement came three days before the Iowa caucuses, when the first votes are cast for the presidential nominations.
The Clinton campaign demanded that all of her emails be released by the state department.
"We firmly oppose the complete blocking of the release of these emails. Since first providing her emails to the state department more than one year ago, Hillary Clinton has urged they be made available to the public. We feel no differently today," said Brian Fallon, secretary of Hillary for America National Press.
"This flies in the face of the fact that these emails were unmarked at the time they were sent, and have been called 'innocuous' by certain intelligence officials," Fallon said.
The Republican National Committee (RNC) Chairman Reince Priebus said, "with even more emails on her secret server found to contain 'top secret' information, Hillary Clinton has removed all doubt that she cannot be trusted with the presidency."
"Hillary Clinton's attempt to skirt government transparency laws by relying exclusively on an unsecure email server in her basement put our national security and diplomatic efforts at risk," Priebus said.
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