Samuel Kunz, who has confessed to having worked at the Belzec extermination camp in German-occupied Poland in 1942-3, was informed of the charges last week, a spokesman for prosecutors in the western city of Dortmund told AFP.
He has also been charged over the deaths of another 10 Jews in two separate incidents which also allegedly occurred at Belzec, said the spokesman, Christoph Goeke.
He has been called as a witness in another Nazi war crimes trial, that of alleged death camp guard John Demjanjuk, 90, a Ukrainian-born former US auto worker deported to Munich from the United States last May.
The Simon Wiesenthal Center, a Jewish human rights organization which helps track down Nazi war criminals, put Kunz at number three in its most wanted list last published in April.
Kunz, whose flat was raided by police in January, denied being personally involved in killing people, prosecutors said at the time of the raid.
A spokesman for a court in Bonn where the charges were filed said that Kunz was 88-years-old. Other reports have put his age at 89 or 90.
Since the Nuremberg trials after the war, where several top Nazi henchmen were sentenced to death, German authorities have examined more than 25,000 cases but the vast majority never came to court.
But now, with many of the suspected war criminals in their nineties, there has been a flurry of arrests and court cases dealing with war-time atrocities, in what Nazi-hunters say is a welcome change of policy in Berlin.
The most high-profile case is that of Demjanjuk, whose trial began last November on charges of assisting in the murder of 27,900 people while allegedly a guard at the Sobibor death camp. He denies the charges.