The 52-year-old's colleagues made the discovery after his wife rang the police station where he worked in Kempten, Allgäu, to ask for help after an argument at home.
The call prompted them to search his locker, inside which they found a 1.5-kilo bundle of cocaine worth between €250,000 and €400,000.
Theories began to spread that he had taken the package during a raid – yet policemen confirmed to the Augsburger Allgemeine newspaper that they never went out on an operation alone.
Chairman of German police union (DPoIG) for Bavaria Hermann Benker said the case had to be handled carefully. He said the first step was to identify where the drugs came from.
Police circles are, the paper said, awash with speculation that the top level officer was connected to criminal circles – even the mafia, which is particularly active in the Allgäu region.
Bavaria's state criminal investigations office and the Munich state prosecutor are now investigating.
State prosecutors confirmed they were already handling charges connected to the man, which the Augsburger Allgemeine newspaper reported involved domestic violence.
Green party state politicians called on Tuesday for the matter to be taken on by Bavaria's Interior Minister Joachim Herrmann.
The Social Democrats (SPD) added that they were waiting for an explanation – particularly around claims the mafia could have connections to the Allgäu police.
Police said in a statement on Monday that the find had already led to “changes in personnel” within the Allgäu police force.