Robert Mueller said the agency had “very few” drones and had used them in “a very minimal way” and “very seldom”.
But the director said the FBI was in the “initial stages” of developing drone policies.
In May, President Barack Obama said he would curtail the use of armed drones in operations outside the US.
Under the new policy described by the White House, the US will only allow drones to be used in areas that are not overt war zones when there was a “continuing, imminent threat” to the US and capture was not feasible.
Wednesday’s acknowledgment that the US federal investigative service has also used drones comes as the nation debates electronic surveillance following the recent disclosure of massive internet and telephone data snooping programmes.
Robert Mueller, who is retiring in July after 12 years as FBI director, described the drone use in testimony in a hearing of the US Senate judiciary committee.
“I will tell you that our footprint is very small,” he said.
He said drones were used in “particular incidents where you need the capability” but said he was unsure how long images captured by the drones were kept.
A surveillance drone was used during a February stand-off with an Alabama man who shot dead a school bus driver and then took a five-year-old boy hostage, according to media reports at the time.
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