The seven email chains from Clinton's time as secretary of state, amounting to 22 separate messages, will be withheld from the public as a result because the information in them is classified at the highest level as "top secret," State Department spokesperson John Kirby said.
The announcement came three days before the Iowa caucuses, when the first votes are cast for the presidential nominations and where Clinton is locked in a tight race with Vermont Senator Bernie Sanders to become the Democratic nominee for the November election.
"These documents were not marked classified at the time that they were sent," Kirby said. He added that the department was now investigating whether the information in them was classified at the time it passed through her private clintonemail.com email account run on a server in her New York home.
The department and intelligence officials have been arguing about the emails, which are being made public under a federal court order, for at least five months. The State Department initially maintained that Clinton might have obtained the same information independently through non-classified channels.
The decision to no longer pursue this argument will add to the questions Clinton has faced for months over her handling of sensitive government information as she seeks to maintain her position as the favourite to become the Democratic nominee.
The Clinton campaign criticised the State Department's decision as the result of "bureaucratic infighting" and "over-classification run amok," adding that the emails should be released.