"A charge of manslaughter has been filed against the defendant," a court transcript said.
The accused, named as Ben Deri, denied the charge against him.
Nadeem Nuwarah, 17, was killed on May 15 during a day of clashes in Beitunia, southwest of Ramallah, between Israeli forces and Palestinian protesters marking the anniversary of what the Arabs term the Nakba, or "catastrophe" of the 1948 creation of Israel.
Footage recorded by US broadcaster CNN captured a group of five or six border police officers in the area, one of whom could be seen firing at the time when the youth was hit.
A justice ministry statement challenged Deri's assertion that he fired only rubber bullets, in accordance with instructions.
"He deliberately fired a live round at the centre of the deceased's body, while intending at the least to cause him serious injury with the forseeable possibility of his death and while concealing his actions at the time," it said.
"With these actions the accused caused, through a forbidden act, the death of the deceased," the charge sheet read.
At the time, Israel said border police were quelling a violent demonstration by about 150 Palestinians, and denied live rounds were used.
Palestinian leaders accused Israel of Nuwarah's "deliberate execution", after CCTV footage appeared to show he was shot unprovoked, during a lull in the violence.
A second teenager, Mohammed Udeh, 16, was killed on the same day in the same place. He was also hit in the chest by a bullet but his family refused to allow a post-mortem.
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