"Sami Lushtaku put the pistol to the prisoner's head behind his left ear and he shot him," protected Witness D is quoted as having told the prosecution. "He fell to his knees and Sami shot him twice more in the head."
Lushtaku's defense lawyer, Arianit Koci, called the indictment "baseless" and said he would object to it.
Selimi, a former top military rebel commander, faces four charges of war crimes, including beating detainees with fists and wooden sticks, and being part of a group of rebels that pinched a detainee's "genitals with an iron tool and subsequently dragged him on the floor with it," according to the indictment.
Selimi's lawyer, Tome Gashi, said his client will plead innocent.
"It is impossible for these things to have happened," Gashi told the AP in a telephone interview. "This was at the time when my client was busy having hundreds of meetings with international officials to end the war with Serbia."
Salustro also alleged that two other suspects, Sahit Jashari and Sabit Geci, allegedly used a chain saw to behead a Serbian policeman, Ivan Bulatovic, in June 1998. The indictment says Bulatovic was taken off a train by three Kosovo Liberation Army soldiers in May 1998, according to a statement given by his wife, Mira Bulatovic, to EU justice officials in 2012.
Bulatovic was kept in detention and frequently walked to a village square by Jashari for people to beat him in public, according to a witness described in the indictment as Witness C.
Sometime in June 1998, Geci "took the chain saw and beheaded Bulatovic with it. Then Geci made some deep cuts into Bulatovic's chest, thigh and legs," according to the witness testimony quoted in the indictment.
The EU rule of law mission, known as EULEX, prosecutes war crimes and organized crime in Kosovo. EULEX works alongside Kosovo justice authorities, but the two have often clashed because the mission has targeted high-profile individuals and former rebels, some of whom are considered heroes by majority ethnic Albanians.