Instead, the 22-year-old infantryman has been given immunity from prosecution in the case. He is required, however, to testify against his fellow Marines.
Mendoza was expected to take the stand Tuesday at a preliminary hearing for Lance Cpl. Stephen Tatum, one of three Marines charged with murder in the deaths of 24 Iraqis in Haditha in November 2005.
There are at least seven Marines to receive immunity in the case.
Mendoza told investigators in March 2006 he shot at least two men because they were in houses declared hostile.
Several members of the squad assaulted the homes in a search for insurgents after a roadside bomb blast killed one Marine.
Mendoza said he and several other Marines, including Tatum, went to a house soon after the blast. There, Mendoza told investigators, he shot a man in a room who was standing by a closet.
"He opened the closet door with his left hand and was reaching inside with his right hand while looking at me. ... I shot him several times," Mendoza in a statement. "I never said anything to him."
Mendoza said he shot another man through a glass door in a different house.
"I was following my training that all individuals in a hostile house are to be shot," Mendoza told investigators.
Mendoza was given immunity Dec. 18, just days before the Marine Corps announced murder charges against four enlisted men and dereliction of duty charges against four officers.
Tatum is charged with murdering two Iraqi girls and killing other civilians in Haditha. At the opening of his hearing Monday, his attorney said Tatum believed he was following procedure by confronting a threat with deadly force.
Besides unpremeditated murder, Tatum is charged with negligent homicide on suspicion that he unlawfully killed two men, a woman and a young boy. He is also accused of assaulting another boy and a girl. If convicted of murder, he faces up to life in prison.
The squad leader, Staff Sgt. Frank Wuterich, is charged with murdering 18 Iraqis. His preliminary hearing is set for Aug. 22.
After the Article 32 investigation, the military equivalent of a grand jury proceeding, hearing officer Lt. Col. Paul Ware will assess the evidence against Tatum and recommend whether he should face a court-martial. The final decision rests with Lt. Gen. James Mattis, the general overseeing the case.
"Knowing what I know now, I feel badly about killing Iraqi civilians who may have been innocent," Tatum told Navy investigators in March 2006. "But I stand fast in my decisions that day, as I reacted to the threats that I perceived at that time."