Mexican officials said that according to witness statements, the US agents on bicycle pursued the youths towards Mexico and that two of them opened fire.
Mexican state police had earlier provided a different version of events, saying the boy had been playing with two other youths on the Puente Negro bridge spanning the Rio Grande, linking Ciudad Juarez to El Paso.
Ciudad Juarez's attorney-general's office also said the youths were playing when they strayed into US territory inadvertently, and ran back towards the Mexican side after being surprised by the US agents.
The victim's parents said their son was killed inside Mexico and that he had no intention of crossing the border.