The indictment was issued on Wednesday against Frane Drlje, Bozidar Krajina and Igor Beneti, the county office of the Chief State Prosecutor stated on its web site on Thursday.
The prosecution decided to stop the investigation against Berislav Garic due to a lack of evidence.
The prosecution also requested the separation of the further criminal proceedings against a wartime special police commander, Zeljko Sacic, who is accused of failing to do anything to prevent the crimes in Grubori or to punish perpetrators.
Drlje, Krajina and Beneti are believed to have been the perpetrators of crimes in Grubori where six Serb villagers were killed and several houses and barns set on fire on 25 August 1995.
According to a press release on the web site of the county office of the Chief State Prosecutor, Drlje is also suspected of having set on fire several houses in the village of Ramljani a day after the atrocity in Grubori.
Drlje, Krajina and Beneti were members of the special police groups that searched the ground for remaining enemy forces in a wider Knin area. After raiding Grubori, Drlje and Beneti opened fire from the weapons at civilians and burnt their houses, the prosecution said adding that some other members of the group under Drlje's command also participated in the crime.
Although the prosecution requested the prolongation of the suspects' detention in custody, they were released from the Remetinec prison on Thursday evening pending the commencement of the trial.
This February, Zeljko Sacic was released from Zagreb's Remetinec prison after spending two months in custody.
Sacic, suspected of covering up the murder of the six Serb civilians in Grubori, was released after all witnesses were heard, as Zagreb County Court investigating judge Zdenko Posavec decided that there was no risk of him tampering with the witnesses, which was why he had been remanded in custody.
Tens of witnesses have been interviewed so far.