The recruitment and tasking of Americans by the group known as the Islamic State, or ISIL, is increasingly taking place "through mobile messaging apps that are end-to-end encrypted, communications that may not be intercepted, despite judicial orders under the Fourth Amendment."
"There is simply no doubt that bad people can communicate with impunity in a world of universal strong encryption," he added.
The op-ed in the Lawfare blog comes ahead of testimonies by Comey before the Senate intelligence and judiciary committees on Wednesday.
The article by Comey reflects an ongoing dispute between the U.S. government and tech companies over the encryption of their products.
Tech companies have asked President Barack Obama not to pursue any policy or proposal that would weaken encryption or create encryption work-arounds.
The Information Technology Industry Council and Software & Information Industry Association, which represents many large tech companies, including Apple, Google and Facebook, said last month such moves would erode consumers' trust in the products and services they rely on for protecting their information.
Google, for example, claims that over 80 percent of its outbound Gmail messages to other providers and 54 percent of inbound mail from other providers were already encrypted, as more providers have enabled and maintained their support for the technology.
"When the government's ability--with appropriate predication and court oversight--to see an individual's stuff goes away, it will affect public safety," Comey warned.
The official said that Americans may well decide that people involved in public safety will be able to do their job well enough despite universal strong encryption. "Those are decisions Americans should make, but I think part of my job is make sure the debate is informed by a reasonable understanding of the costs," he added.