In a letter to the Senate Judiciary Committee, Comey revealed that the bureau was probing additional emails discovered as part of a separate investigation.
Comey wrote: “In connection with an unrelated case, the FBI has learned of the existence of emails that appear to be pertinent to the investigation... I agreed that the FBI should take appropriate investigative steps designed to allow investigators to review these emails to determine whether they contain classified information, as well as to assess their importance to our investigation.”
It was not made clear in Comey’s letter where the new emails came from, or who sent or received them.
Comey added that it was unclear how long the additional review would take, and that the FBI ‘cannot yet assess whether or not this material may be significant’.
Law enforcement sources told US media that the emails were not linked to WikiLeaks or the Clinton Foundation.
The Democratic nominee’s campaign team were on a plane en route to Iowa when the news broke.
A spokesperson for the Clinton campaign told CNN: “We’re learning about this just like you all are.”
The news comes less than two weeks before the Presidential Election on November 8, with Clinton currently leading Republican counterpart Donald Trump in the polls.
Trump praised the FBI’s decision as he addressed a crowd in Manchester, New Hampshire, shortly after the news broke.
The Republican nominee said on Friday that ‘perhaps finally justice will be served.’
Trump said ‘Clinton’s corruption is on a scale we have never seen before,’ adding: “We must not let her take her criminal scheme into the Oval Office.”
Trump said he had ‘great respect’ for the FBI’s decision.
He had previously been very critical of the bureau and the Department of Justice for the decision earlier this year not to bring charges against Clinton.
House of Representatives speaker Paul Ryan said Mrs Clinton has ‘nobody but herself to blame.’
Ryan said in a statement: “She was entrusted with some of our nation’s most important secrets, and she betrayed that trust by carelessly mishandling highly classified information.
“This decision, long overdue, is the result of her reckless use of a private email server, and her refusal to be forthcoming with federal investigators.
“I renew my call for the director of national intelligence to suspend all classified briefings for secretary Clinton until this matter is fully resolved.”
Clinton’s vice presidential nominee Tim Kaine gave little away when asked about the new probe, saying he had to ‘read a little more’ when asked about the developments at an early voting site in Tallahassee, Florida.
The controversy first came to light in March 2015 when the State Department’s inspector general revealed that the Democratic presidential nominee had used personal email accounts on a private server - rather than email accounts managed on federal government servers - during her time as Secretary of State.
Political opponents and some members of Congress claimed that Clinton’s actions had contravened State Department protocols and regulations concerning recordkeeping.