It is the first time a U.S. intelligence official has publicly acknowledged Pentagon or CIA drone operations in Libya prior to the terrorist strike on the consulate last year.
The disclosure could intensify GOP criticisms that the administration did not act quickly enough to protect Americans in the consulate during the attack.
Clapper testified alongside CIA Director John Brennan, FBI Director Robert Mueller and Defense Intelligence Agency chief Lt. Gen. Michael Flynn during Thursday's hearing on potential threats facing the United States.
Clapper did not provide details on what kind of Department of Defense drones were used during those operations, where they were based or how long those drones had been flying before the Benghazi attack.
The Pentagon also has yet to comment on the drone missions it carried out in Libya.
Washington reportedly deployed surveillance drones to Benghazi after the consulate strike, which ended with the deaths of U.S. Ambassador Chris Stevens and three other Americans. But news reports at the time also claimed a Predator drone was flying over the consulate during the attack.
Rep. Michele BachmannMichele Bachmann'Real Housewives' producer 'begging' Conway to join cast Ex-rep admires furs amid PETA inaugural gala Why Republicans took aim at an ethics watchdog MORE (R-Minn.) pressed the witnesses on the drone missions in Libya on Wednesday, suggesting those operations could have spurred the deadly consulate attack.
Brennan, though, declined to provide further details on whether U.S. drone operations in Libya before the Benghazi attack included airstrikes.
"I don't know what it is specifically you're referring to, but ... I would defer to the White House on whatever happened at that time," Brennan told Bachmann.
"I'm just wondering if the State Department or if the military was aware or if the CIA was aware," she asked about the possibility of armed drone strikes in eastern Libya.
"If we aren't going to talk about that, we aren't going to talk about that. But that's a question I'd like to know," Bachmann added.
After the hearing, Bachmann told The Hill her office had not directly received any intelligence suggesting American armed drone strikes were carried out in Libya before last September's attack.
But recent accounts by former U.S. special forces members prompted Thursday's line of questioning, she added.
News reports last year suggested the diplomatic mission of the U.S. Consulate in Benghazi was a cover for a large-scale CIA intelligence operation inside Libya run out of the State Department facility.
The spartan outpost in Benghazi was reportedly one of several intelligence hubs set up by Langley in the aftermath of the Libyan revolution that ended with former dictator Moammar Gadhafi's death in March 2011.
The Obama administration initially claimed the Benghazi attack was the result of an anti-American protest gone wrong. Only weeks later did the Obama administration acknowledge the strike was a planned, coordinated attack by Islamic extremist groups in the country.
Republican lawmakers have charged that the administration sought to downplay the terrorist attack in the weeks ahead of last November’s presidential election.
On Thursday, the mother of a State employee slain in Benghazi endorsed Republican calls for a select committee to investigate the attack.