The indictment against former Defence Minister Khaled Nezzar, who is believed to live in Algeria but who could be tried in his absence, relates to alleged crimes committed between 1992 and 1994 the statement said.
Swiss-based non-governmental organization TRIAL International brought a criminal complaint against Nezzar under a law passed in Switzerland in 2011, which allows prosecution for serious crimes committed anywhere, under the principle of universal jurisdiction.
Reuters could not immediately contact Nezzar, or a Geneva-based lawyer who has previously represented him, for comment. Nezzar has previously denied accusations of wrongdoing during the war in comments to Algerian media. Nezzar was arrested in Geneva in 2011, but he was released after two days of hearings and was believed to have returned to Algeria.
The new indictment means there will be a trial even if Nezzar, who is in his 80s, is not present, TRIAL International said.
The Attorney General's office said its investigations had been "complex" and at one stage temporarily abandoned the proceedings amid questions over its own jurisdiction to assess alleged war crimes.
Nezzar is set to be the highest-level military official ever to be tried using universal jurisdiction laws, according to TRIAL.
It would be one of only a handful of such cases to be heard in Switzerland and the second-ever hearing for crimes against humanity after a case against a Liberian warlord concluded this year.
Nezzar became Algeria's defence minister in 1990 and was involved when its military seized power the following year and overturned a parliamentary election that had been won by the Islamic Salvation Front.
The ensuing violence, dubbed the "dirty war," lasted until 1999 and some 200,000 people died, mainly civilians massacred by groups the military said were Islamist fighters.