Retired general Atif Dudakovic and 16 others were accused of "crimes against humanity" including the "murder of more than 300 ethnic Serbs" as well as "persecution and maltreating of civilians and prisoners of war," Bosnia's prosecutor's office said in a statement.
The suspects were all members of the mainly Muslim Bosnian army fifth corps, commanded by Dudakovic.
The unit was operating in western Bosnia, a region which was completely surrounded by Serbian forces from Croatia and Bosnia.
The ethnic Serb victims were "mostly elderly civilians, as well as prisoners of war who either surrendered or were arrested," the statement added.
The 17 suspects were also charged with destroying 38 Orthodox churches and other religious targets.
The indictment against Dudakovic, now 64, also refers to crimes against Bosnian Muslims in the region of Bihac and Cazin, the prosecutors said.
Although Bosnia's 1992-1995 war was fought between its three main ethnic communities -- Croats, Muslims and Serbs -- in this region Bosnian Muslims also clashed with each other.
Commanders of Bosnian forces have rarely been tried for war crimes.
Two chiefs of staff, General Rasim Delic and Sefer Halilovic, were tried by the UN tribunal in The Hague.
Delic was sentenced to three years in prison by the international court in 2008 but died while awaiting an appeal verdict.
Halilovic was acquitted in 2005.
Muslim wartime commander of Srebrenica, Naser Oric is being retried on war crimes charges.
Oric was acquitted last year by a Sarajevo court of killing three Serb prisoners at the start of the war, but that ruling was overturned in June for procedural reasons.
Bosnia's 1992-1995 war claimed some 100,000 lives.
Local authorities are allowed to try low-profile war crimes cases while a UN tribunal, which has now closed, was tasked with hearing cases involving top wartime officials.
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