Rhymefest, whose legal name is Che Smith, posted a video in which he argues with officers at the front desk.
"You wonder we don't report crimes? The police treated me disgustingly," Smith tweeted along with the video.
Chicago Police Department spokesman Anthony Guglielmi tweeted back in response, "@RHYMEFEST disappointing to say the least. On behalf of CPD, I apologize for how you were treated. We will be addressing this today."
The video, recorded in a police station near the rapper's home, begins with him already talking with an officer at the front desk. She tells him he cannot record while in a police station.
He continues to record and begins to talk to another officer who says a supervisor told him to ask the rapper to leave.
Rhymefest continues to talk with the officers and complains about the first officer's attitude when he came to the desk to file a robbery report.
Eventually the second officer tells Rhymefest they will take his report.
Guglielmi told CNN that Chicago Police Chief of Patrol Fred Waller called Rhymefest to apologize and Superintendent Eddie Johnson told Waller to address the incident with officers in the district.
The rapper said he was in his car at 7:35 a.m. Saturday when someone got in and put a gun to his head, told him they were going to shoot him and demanded his wallet. The thief ran away, Rhymefest says.
He tweeted messages to the robber.
"When you look in my wallet & see the name Che Smith on the ID. DM me, yes contact me apologize and talk to me like a brother," he wrote. "Give me faith that it's our desperation & not our hearts thatre dark. The man who robbed me I want to reach out to me If I know him tell him."
Rhymefest said he had $3 in his wallet.
He won a Grammy and an Academy Award in 2015 for his work with Common and John Legend writing the song "Glory," featured in the film "Selma."