The boy, Mason Campbell, will be tried as a juvenile in connection with what authorities have described as a planned attack at Berrendo Middle School in Roswell, said New Mexico State Police Lieutenant Emmanuel Gutierrez.
Campbell is accused of taking a 20-gauge shotgun from his home and modifying it. With the weapon concealed in a duffel bag, he entered the school gymnasium and opened fire on students waiting for classes to start on Tuesday, police said.
Police have not revealed a motive for the attack, and investigators continue to look into the possibility that Campbell warned some friends before the shooting.
The charges against the boy were filed in children's court on Wednesday in the state's Fifth Judicial District Court. In accordance with New Mexico law, no one under age 14 in the state can face adult sanctions.
Two of the battery counts against Campbell stem from the wounding of two children in the attack, while the third is for an adult staff member who was slightly wounded and declined medical aid, police said.
An 11-year-old boy and a 13-year-old girl were seriously wounded and airlifted to the University Medical Center in Lubbock, Texas, where the boy was in critical condition and the girl was listed as satisfactory on Wednesday.
A hospital spokesman on Thursday said the facility would not be releasing any more information on their conditions until further notice.