The complaints include allegations that people were called racial slurs, not informed of their rights and forced to sign their names to documents.
The Department of Homeland Security oversees a program in which participating law enforcement agencies assist the federal government on immigration policies.
The Wake County Sheriff's Department has been taking part in the federal program to deport dangerous felons since 2009. Any illegal immigrants arrested by deputies are reported to federal immigration authorities and are eligible for deportation.
A spokesperson for the ACLU says the organization is pleased the complaints are being investigated, even if it's been more than a year since the group called for the investigation.
Wake County Sheriff Donnie Harrison says he's confident his office is operating by the book. He says the sheriff's office is already looking into the complaints.