Comey said the revelations about widespread surveillance have led to a climate which could hinder the ability to catch criminals and terrorists, underscored by new efforts to encrypt smartphones to make them inaccessible to investigators, even with a warrant.
"Perhaps it's time to suggest that the post-Snowden pendulum has swung too far in one direction -- in a direction of fear and mistrust," Comey said in a speech at the Brookings Institution.
Comey's comments sought to renew the debate about the FBI "going dark," or being unable to access encrypted calls and messages from new apps and services which fall outside the traditional realm of "wiretaps."
The FBI had been calling for changes to the US law covering wiretapping in 2013, but that debate was shelved after the revelations from former NSA contractor Snowden in June 2013 about vast surveillance of telephone and online communications.
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"In the wake of the Snowden disclosures, the prevailing view is that the government is sweeping up all of our communications. Of course, that's not true," he said.
"And if the challenges of real-time interception threaten to leave us in the dark, encryption threatens to lead all of us to a very dark place."
Comey said the announcements in recent weeks by Apple and Google to encrypt their smartphones so that law enforcement cannot access them, even with a warrant, provided a "catalyst" for him to revive the debate from 2013.
Comey last month warned that the new encryption by default could lead to problems for law enforcement, even as privacy activists applauded the efforts by the companies.
In his Brookings comments, Comey said he was not looking for a "back door" into devices and systems which could be exploited by malicious actors.