At Boston College's cybersecurity conference Wednesday, Comey said that he a fan of "strong encryption" but noted that "it is making more and more of the room of what the FBI investigates dark."
Between September and November, the FBI received 2,800 devices it had lawful authority to open but could not open 1,200 of them "with any technique," he said.
He said there needs to a balance between privacy and the FBI's ability to lawfully access information, a conversation that he acknowledged will require some "humility" on the part of the bureau.
"We need to stop bumper-stickering each other. This isn't the 'FBI versus Apple,'" he said.
"We need to build trust between the government and private sector."
Comey also addressed the need for the FBI to recruit top computer talent who might otherwise head to Apple or Google but joked that the bureau isn't resorting to "beanbag chairs and granola" to draw Silicon Valley whiz kids.
He said new hires do appreciate the FBI's culture.
"We are dogged people," he said. "We just gave up on D.B. Cooper, and that was after 50 years."
And Comey, who is three and a half years into a 10-year term, referenced his own doggedness.
"You're stuck with me for another six and a half years," he quipped.