New Mexico Gov. Susana Martinez said at a news conference Tuesday afternoon a male 12-year-old student was in critical condition and a female 13-year-old student was in serious condition following the shooting in the Berrendo Middle School gym about 8 a.m. MST.
Both victims were initially taken to a Roswell hospital for treatment but were then airlifted to University Medical Center in Lubbock, Texas, KRQE-TV, Albuquerque, reported.
The TV station reported a witness described the shooter as a nice kid who played on the school football team.
Martinez said a school staff member sustained minor injuries and declined medical treatment after helping disarm and subdue the suspect, a seventh-grader who police said carried a shotgun into the school. The governor said the staff member "walked right up to [the shooter] and asked him to set down the firearm, which he did."
The names of the victims and the suspect had not been released. Police said they had contacted the shooter's parents.
The FBI was assisting in the investigation.
New Mexico State Police Chief Pete Kassetas said police did not yet know what the motive for the shooting might be.
"I believe we have the only individual in custody right now who is responsible for this," he said.
Kassetas said State Police Lt. Gary Smith was dropping his child off at school when Principal Susan Martin enlisted his help.
By the time Smith reached the gym, the shooter had already put the shotgun down, he said.
"I commend the principal and the people who work at the school for saving many lives," Kassetas said.
The school was under lockdown and officials urged parents or guardians not to go to the facility. Students were transferred from the school to a mall to be picked up.