He is ranked third on the Simon Wiesenthal Center's list of most-wanted Nazi suspects.
War crimes trials
The former guard has also been called as a witness in the war crimes trial of alleged Nazi death camp guard John Demjanjuk, a Ukrainian-born former US car worker.
Demjanjuk, also aged 90, is currently on trial in Munich on charges of being an accessory to the murder of 28,060 Jews as a guard at the Sobibor death camp in occupied Poland.
He denies he was ever a camp guard.
Prosecutors have alleged that both Kunz and Demjanjuk trained as guards at the Trawniki SS camp.
German authorities have examined more than 25,000 cases relating to Nazi war crimes since the end of the war, but the vast majority have never gone to court.
However in recent years, 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.
Efraim Zuroff, a Nazi hunter at the Simon Wiesenthal Center, said the indictment of Kunz was "a very positive development".
"It reflects recent changes in the German prosecution policy, which have significantly enlarged the number of suspects who will be brought to justice."
German prosecutors said the case against Kunz has been sent to the state court in Bonn, where officials were considering whether and when to hold a trial.