The FBI has collected 430,000 iris scans in the past three years, leading privacy campaigners to question the project.
What started as a pilot in 2013 has grown into a database “without any public debate or oversight”, said the American Civil Liberties Union.
It amounted to “runaway surveillance”, director of technology Nicole Ozer tweeted.
The FBI said it was developing “best practices” for iris image capture.
The project was launched in September 2013 and has seen the FBI collaborate with agencies in Texas, Missouri and California.
The iris data, taken from people who have been arrested, can be scanned in a fraction of a second.