In a letter to several U.S. congressional committee chairmen, Federal Bureau of Investigation Director James Comey said the agency will determine whether the emails contain classified information, adding that it is unclear how significant the new materials may be.
Comey said he "cannot predict how long it will take us to complete this additional work."
The announcement shook up the campaign for the Nov. 8 election, where Clinton is the Democratic Party's candidate and the front-runner in opinion polls.
The FBI spent about a year investigating Clinton's use of an unauthorized private email server for her work as U.S. secretary of state between 2009 and 2013 after it emerged that there were classified government secrets in some of her emails.
In July, the FBI characterized Clinton's handling of classified information via email as "extremely careless" but, after a months-long investigation, it recommended that no criminal charges be brought.
Comey provided no further details on Friday about the nature of the additional emails now being looked into.
"In connection with an unrelated case, the FBI has learned of the existence of emails that appear to be pertinent to the investigation," Comey wrote in the letter released on Friday.
He said that the FBI "cannot yet assess whether or not this material may be significant."
Spokespeople for Clinton did not immediately respond to a request for comment. She has previously apologized for her server, which was set up in her home in Chappaqua, New York. She said the arrangement was a mistake, and that she did not knowingly send or receive classified information.
Friday's news was seized upon by Donald Trump, Clinton's Republican rival for the presidency, who has repeatedly sought to cite her email practices as disqualifying her for office.
"I need to open with a very critical breaking news announcement," Trump said at the start of a rally in Manchester, New Hampshire, before describing Comey's letter.
He was drowned out by a chant from the crowd: "Lock her up!"
"We must not let her take her criminal scheme into the Oval Office," Trump continued. "I have great respect for the fact that the FBI and the Department of Justice are now willing to have the courage to right the horrible mistake that they made."
Paul Ryan, the House of Representative Speaker and the most senior elected Republican in Congress, said Clinton should not get classified briefings until the investigation was over.
"Yet again, Hillary Clinton has nobody but herself to blame," he 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."
U.S. stock prices fell along with U.S. Treasury yields at midsession on Friday after the FBI news.
The U.S. dollar slipped against major currencies such as the euro and the yen, while the Mexican peso fell to an 11-day low.
A victory for Trump has been viewed as a risk for the Mexican currency given his promises to clamp down on illegal immigration and rethink trade relations.