Republicans have seized on the news to denounce her candidacy, while Clinton campaign chair John Podesta said the FBI "owes the American public" the full details of what it has found to clear up any whiff of controversy so soon before the election.
In a statement on Friday, Mr Comey said: “In previous congressional testimony I refer to the fact that the FBI has completed its investigation of former secretary Clinton’s personal email server.
"Due to recent developments I am writing to supplement my previous testimony.
"In connection with an unrelated case the FBI has learned of the existence of emails that appear to be pertinent, and I am writing to inform you that the investigative team briefed me on this yesterday and I agreed 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."
He said he "cannot yet assess whether or not this material may be significant", and did not say how long the investigation would take.
Few details are available. The emails were found on a government computer and were not related to WikiLeaks.
FBI director says 'no charges' for Hillary Clinton amid email scandal
The email controversy has dogged Ms Clinton's campaign for months.
She repeatedly said she handed over 33,000 emails to the FBI and the Justice Department to determine whether she had sent or received top secret or classified information on an unsecured server.
The FBI also denied a "quid pro quo" arrangement with the state department to downgrade certain information in the emails from "classified" to "unclassified".
Trump Blasts Clinton Over Leaked DNC Emails
Mr Comey told the Justice Department in July that although Ms Clinton had displayed "extreme carelessness" which could have lead to adversaries hacking her account, he did not recommend any criminal charges.
The Justice Department agreed with the FBI's recommendation the same month.
As the news broke, Ms Clinton was flying to Iowa to speak alongside women's rights leaders at two rallies. Ms Clinton did not comment on the news during her first rally Friday afternoon at Cedar Rapids.