The three indictees - Slobodan Medic, Pera Petrasevic and Branislav Medic - are accused of killing six Bosniaks at Trnovo, eastern Bosnia.
The other two indictee - Aleksandar Meduc and Aleksandar Vukov - are treated as accomplices in the crime.
All of them were members of the notorious Scorpions unit.
The indictment was issued on the basis a video showing members of the Scorpions unit killing six civilians from Srebrenica, four of whom were underage.
The video footage was shown for the first time during the war crimes trial against Slobodan Milosevic before the International Criminal Tribunal for the former Yugoslavia (ICTY) in The Hague.
The sixth perpetrator, who was also identified from the amateur video tape, Slobodan Davidovic, has been sentenced to 15 years in prison in Croatia for war crimes.