A Mexican official with direct knowledge of the investigation confirmed the boy was shot by the agent, and said authorities were meeting Friday in Mexico City to discuss the case. The person also said the teenager had been shot multiple times in the back. The person spoke on condition of anonymity because they were not yet authorized to discuss details of the case.
Mexico's Foreign Relations Department issued a statement Thursday saying it "forcefully condemned" the shooting and calling such deaths "a serious bilateral problem."
Border agents are generally allowed to use lethal force against rock throwers, and there are several ongoing investigations into similar shootings in Arizona and Texas.
Associated Press writer Elliot Spagat in San Diego contributed to this report.