At the hearing on Monday, the officer was charged with two counts of illegal use of a weapon, two counts of inappropriate behaviour and exceeding his authority and one count of obstruction of justice, Israeli military sources said.
The indictments followed a military police investigation into an
incident on 5 October in which 13-year-old Iman al-Hams was shot dead by soldiers in the southern Gaza town of Rafah on suspicion she was carrying explosives in her school satchel.
According to a fellow soldier, the commander then fired into the girl's body several times. The doctor who examined the body said it was riddled with 20 bullets, including five in the head.
The indictments were issued just five weeks after the soldier was cleared of any wrongdoing in another parallel army investigation.
Israeli soldiers have been accused
of heavy-handedness in Palestine
"The investigation did not find that the company or the company commander had acted unethically during the incident," the army said on 15 October following the conclusion of an internal investigation.
The soldier was arrested shortly afterwards by the military police after they discovered contradictions in his testimony, public radio said.
The officer denies all the charges against him, the radio said, adding that tapes of the radio communications on the day are to be played at the trial.
Army chief of staff Moshe Yaalon said soldiers had justified firing at the girl because they suspected she wanted to distract their attention and lead them away from their watch tower so Palestinian snipers could shoot them.