Federal officials sent a letter to the county, saying they are increasingly concerned about the use of force and alleged abuse of prisoners by jail deputies and staff.
According to the Justice Department, this is a separate investigation from the F.B.I's ongoing criminal probe.
The F.B.I. has been looking into allegations of beatings and other misconduct in the jails following complaints by the American Civil Liberties Union. The non-profit organization said one of its jail monitors saw deputies beat an inmate unconscious.
The Los Angeles County Sheriff's Department says it will cooperate fully with the new investigation.
"We are here to help, and we have nothing to hide," said Sheriff's spokesman Steve Whitmore. "We welcome anybody to look at anything that we are doing, and we have made significant improvements over the last several years when it comes to the use of force."
The civil rights probe will also take a critical look at the conditions provided for mentally ill inmates.