In a petition filed at the state prosecutor's office in Hamburg, Heinz Uthmann, judge at the Labour Court in Hamburg, has charged Merkel with "rewarding and approving an intentional homicide".
In her initial reaction to the death of bin Laden, Merkel told journalists in Berlin on Monday she was quite pleased that the al Qaeda leader was killed.
"This remark is astonishing for the daughter of a pastor and stands apart from all values such as human dignity, compassion and rule of law," said the petition, which was filed on Thursday.
It claimed that the "initial suspicion of a criminal offence" is justified.Uthmann, who has been working as a judge at the Hamburg Labour Court for the last 21 years, said in a newspaper interview, "I am a law-abiding citizen and as a judge I defend the rights and rules".
He described Merkel's comments as "undignified and tasteless".
The assumption that the US special forces' mission was not to kill bin Laden but to execute an international arrest warrant is out of place because under the the international law the American forces have no authority for that in Abbottabad, the petition said.
Hamburg's chief state prosecutor Wilhelm Moeller said he expected the case to be handed over to concerned authorities in Berlin.
Merkel faces upto three years in jail if the charges against her are established, media reports said.
Chancellor Merkel was rebuked by leaders of Germany's Catholic and Protestant churches and several leading politicians, including her own party colleagues, for her remarks.
A government spokesman tried to play down the controversy by suggesting that Merkel had the victims of al Qaeda attacks in her mind when she spoke about bin Laden's death.
