He made the stark comments at the International Chiefs of Police Conference in San Diego, speaking before thousands of law enforcement officials from across the United States and overseas.
Fueled by images and videos of police encounters posted online, "good people" have come to believe that "biased police are killing at epidemic rates," with black men and women the overwhelming victims.
Most recently, violent protests broke out in Charlotte, North Carolina, after police fatally shot a black man who authorities said appeared to have a gun. Parts of the incident were captured on cell phone video and police dash-cam video.
"Each video becomes further proof of an epidemic nationwide of police brutality," Comey said.
But "however good their hearts," they have "no idea of whether the number of black people ... being shot by police is up, down or sideways" in recent years, Comey insisted. "They have no idea of these things because we [in federal government] have no idea of these things."
He noted that "in the absence of information we have anecdotes," and a "small group of videos serves as an epidemic."
This narrative has "real costs" -- it is making it harder for police to do their jobs and protect the communities they have sworn to protect, and it is making it harder for police departments to recruit new officers.
He said Americans across the country will be "deeply, deeply sorry" if people stop choosing to serve the country through law enforcement.
While "there are bad cops," such bad apples exist in all industries, he added.
"The truth is this: Police officers are overwhelmingly good people," and they took dangerous jobs because they want to help people, Comey said.
So to close the growing chasm between police and certain communities, the country needs to have an informed debate about policing based on reliable information.
"If we do those things and if we do them well, we will save lives," he said.
The FBI and Justice Department have vowed in the next couple of years to create a national database detailing police shootings and other uses of force by federal, state and local law enforcement.