The 41-year-old Hamburg officer whose name has not been released, is said to have lost control and hit a 20-year-old who had been arrested, several times on the head, according to the Hamburger Morgenpost newspaper.
The man, based at the well-known Davidwache station in central Hamburg, has been moved while the investigation is conducted.
The incident occurred on Wednesday night, the paper reported. The officer was on duty in the station when some of the 12 officers who work under him, brought in the young man having arrested him on the Reeperbahn for alleged fraud.
As the young man was being brought in, he attacked the officers, injuring one woman officer so badly she had to be taken to hospital for treatment.
When the other officers were searching him, their boss came into the room and punched him several times in the head. His deputies reported him, and the case is being looked at by the police internal investigations office.