The prosecutor's statement on Tuesday said Milomir Savcic willfully aided ex-Bosnian Serb army commander Ratko Mladic and others during the atrocity, which has been described as a genocide by two international courts and is considered the worst crime to have taken place in Europe since World War II.
Bosnian Serb forces led by Mladic attacked Srebrenica on July 11, 1995, separated men from women and children and killed about 8,000 Muslims, who were then buried in mass graves.
Savcic is accused of commanding troops to capture, imprison, kill and bury hundreds of Bosnian Muslims at several locations near Srebrenica.
He helped Mladic and colonel Ljubisa Beara, as well as other commanders of the Drina Corps and Zvornik Brigade, which executed the massacre, to destroy the Muslim men as an ethnic group in the area, the prosecutor said in a statement.
Both Mladic and Beara were jailed for life for the genocide by the International Criminal Tribunal for the Former Yugoslavia.
The 60-year-old Savcic denied the charges in a statement on Bosnian Serb television, saying his troops captured 28 Bosnian army troops in July 1995 in the area of Nova Kasaba, near Srebrenica, and handed them over to another unit.
Bosnian Serb leader Milorad Dodik, the Serb member of Bosnia's multi-ethnic presidency, claimed the ruling showed bias against Serbs.
Savcic holds both Bosnian and Serbian citizenship and heads the Bosnian Serb war veterans' association. It is not clear if he is in custody.
After the slaughter at Srebrenica, Bosnian Serbs buried their victims in mass graves around the town. Experts are still unearthing the remains.
More than 100,000 people were killed in Bosnia's 1992-95 war between the country's Serbs, Muslims and Croats. Nearly 25 years later, Bosnia remains ethnically divided.