Asked at the Aspen Security Forum in London how much the US agency paid for help to get into the phone, Comey replied, "A lot."
"More than I will make in the remainder of this job, which is seven years and four months, for sure. But it was, in my view, worth it," Comey said.
Based on Comey's salary, listed at about $14,900 a month, that comes to more than $1.3 million for the hack, the results of which have still not been divulged.
A video of Comey's talk was streamed on the Aspen Security Institute website.
Apple and the FBI were headed for a court showdown setting national security needs against privacy principles after the agency took the smartphone maker to court to force it to break into the encryption-protected iPhone 5C.
The phone had been used by Syed Farook, who along with his wife Tashfeen Malik slaughtered 14 people at a party in San Bernardino, California on December 2 before dying in a firefight with police.
Apple, backed by a broad coalition of technology giants like Google and Facebook, was fiercely opposed to assisting the government in unlocking the phone on grounds it would have wide-reaching implications on digital security and privacy.
Comey said the litigation in the case had inspired a "marketplace around the world" for people to break into an Apple 5C running IOS 9, the phone Farook used.
"Somebody approached us from outside of the government and said, 'We think we've come up with a solution.' And we tested and tested and tested it, and then we purchased it."
He acknowledged the fundamental principles in conflict in the case and said he was glad that, at least in this instance, a way outside the court was found.
"Litigation is not a great place to resolve hard values questions that implicate all kinds of things that all of us care about," he said.
"We have a problem where all of us share a set of values that are in conflict. We have to figure out how to resolve privacy and security on the Internet and on our devices with public safety."
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