The probe centers around a January incident at the Twin Towers Correctional Facility.
An ACLU jail observer claims she saw two deputies beating and using a Taser on an inmate as he lay limp.
But an internal sheriff's log offers a different account. It says the inmate was combative and punched deputies.
Sheriff's department spokesman Steve Whitmore said he has no problem with the investigation.
The findings will be presented to the Department of Justice in Washington.