The files date from his time as vice-president and the years between then and his election as president in November 2020.
Robert Hur, a one-time US attorney under former president Donald Trump, will lead the investigation. Republicans in Congress have demanded to see visitor logs for Mr Biden’s home and say the discovery of classified files at one of his residences was a national security risk.
News that sensitive documents dating from his term as vice-president had been found in a private office at the Penn Biden Center, a think tank in Washington, emerged earlier this week.
That was followed by the disclosure that a second cache was discovered at his home. The first batch was found on November 2, but only became public this week.
Kevin McCarthy, the new Republican Speaker of the House, questioned the timing of the disclosures and accused Mr Biden of knowingly mishandling the papers.
“He knowingly knew this happened going into the election, going into interviews. This is what makes Americans not trust their government,” Mr McCarthy said yesterday.
James Comer, chairman of the House oversight committee, said: “We need to know all who have had access to the president.” Colorado Republican Ken Buck urged the White House to release all Mr Biden’s visitor logs.
Mr Trump is also under investigation by the Justice Department after FBI agents found classified files, some marked Top Secret, at his Florida estate last year.