"I'm very glad that the litigation between the FBI and Apple on San Bernardino has ended, because it really was about getting access to that phone," Comey told a conference at Georgetown University, referring to the court case aimed at gaining access to the phone used by one of the shooters in last year's deadly attack.
But Comey said it was still important to have a discussion on the topic because "there is a collision going on between values of all shades between privacy and security."
Comey said he is concerned that defenders of strong encryption, which allows only the users to access data, have failed to consider all the implications.
"We are moving to a place in American life, because we live our lives on these devices (where they) will be immune to the judicial process," he said.
"My only request is that we talk about the costs ... We should not drift to a place where wide swaths of American life become off limits to the judicial process without a serious, adult conversation."
Comey said the FBI has not yet decided whether to tell Apple about how it accessed the data.
Some activists have said the FBI should tell Apple under a US policy aimed at helping tech companies plug security vulnerabilities.
Comey said that "we are in the process of sorting it out, we are close to a resolution but I'm not ready to make news on this.
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