Detailed allegations were released, but the woman's name was withheld, CNN reported Saturday.
The woman, who withdrew a lawsuit against Rogers -- but is expected to re-file the suit -- accused her former boss of having her "perform sexual services," including "masturbating him" and having to watch him parade around nude.
The sexual harassment began soon after she was hired 2003, Rogers' accuser -- a single mother -- said.
She said stayed at her job until May 2012 because she could not find another position "of comparable pay ... and because her child's father abandoned them," the accuser told the police.
"I can tell you that this is an open and ongoing investigating," said Sgt. Gregory Lyon of the Atlanta Police Department.
Court documents have been sealed and both sides in the case have agreed not to discuss details with the media, The Atlanta Journal-Constitution reported.
The Waffle House chain -- founded by the Rogers' father in 1955 -- has 1,500 restaurants. The firm has its headquarters in Norcross, Ga.