A 15-year-old boy was also shot in the head.
Two campuses remained on lockdown for almost two hours after the shooting as parents stood outside hoping to be reunited with their children.
In Los Angeles, students at middle and high schools are required to go through daily random searches for weapons.
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Three other people, ranging in age from 11 to 30, suffered minor cuts and scrapes.
A 12-year-old girl was booked into Juvenile Hall on suspicion of negligently discharging a firearm on school grounds.
The LAPD responded to a 911 call made at 8.55am local time, following reports of shots fired at Sal Castro Middle School in Los Angeles.
Police arrested a female student suspect and recovered a gun.
A 15-year-old boy sustained critical wound to the head while a 15-year-old girl was shot in the arm, NBC News reported.
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The officials weren't authorized to speak on the record and briefed reporters on condition of anonymity. Several children were also affected, the group said.
"This continues to be an active investigation", the LAPD said in a statement tonight.
A Los Angeles police spokesman says a middle-school shooting that injured four children Thursday morning was accidental. Parents who wished to pick up their children early were directed to a baseball field near the school at Loma Drive and Crown Hill Avenue.
It was not immediately clear if she was the student in custody.
The Los Angeles Police Department said it is trying to determine how the 12-year-old suspect allegedly brought a gun to campus.
The classroom shooting is the latest USA gun violence at schools, following a high school shooting in the US state of Kentucky on January 23.
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BBC reports that the Los Angeles Police Department does not believe there is any continuing threat. Some students ran from the classroom as the gunfire started, police said.
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