In his first public remarks since Apple CEO Tim Cook said he would fight the federal magistrate's order, Comey said the Justice Department's request is simply about gaining access to the locked phone.
"We don't want to break anyone's encryption or set a master key loose on the land," Comey said in a posting that appeared on the lawfareblog.org site late Sunday.
Investigators want to hack into an iPhone belonging to the late Syed Farook, a US citizen who along with his wife Tashfeen Malik went on a shooting rampage in San Bernardino, California that killed 14 people on December 2.
Apple claims that cooperating with the FBI probe would undermine overall security for its devices.
"The San Bernardino litigation isn't about trying to set a precedent or send any kind of message," Comey said. "It is about the victims and justice."
According to Comey, the "particular legal issue is actually quite narrow... We simply want the chance, with a search warrant, to try to guess the terrorist's passcode without the phone essentially self-destructing and without it taking a decade to guess correctly. That's it.
The phone may or may not hold important clues. "But we can't look the survivors in the eye, or ourselves in the mirror, if we don't follow this lead," he wrote.
This case highlights the new technology that creates "tension between two values we all treasure: privacy and safety. That tension should not be resolved by corporations that sell stuff for a living.
"It also should not be resolved by the FBI, which investigates for a living. It should be resolved by the American people deciding how we want to govern ourselves in a world we have never seen before."
Finding "the right place, the right balance, will matter to every American for a very long time" said the head of the Federal Bureau of Investigation.
Both Apple CEO Tim Cook and Comey have been invited to testify about encryption on Capitol Hill.
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