Jamaal Smith, 15, came home from Martin Middle School on Wednesday with the injuries. The teen has severe autism and doesn't speak.
"He can't tell us what's going on with him. We're trusting the school to take care with our kid, and here he comes home with his arm broken," said his father, John Smith. "They say he took a hard impact, whatever happened to him."
Interviews with teachers and assistants at Martin Middle indicate Jamaal appeared to be fine when he left school, said Michael Evans, spokesman for the Wake County school system.
"What we're trying to do right now is walk back through the day. The student is in a self-contained classroom and has a very high student-to-adult ratio."
District policy calls for one teacher and one assistant to be present for every six special-needs student, and students with autism are always supposed to be attended.
The private service hired to transport Jamaal to and from school will also be interviewed, officials said.
"I'm not blaming anyone for this, but if it was an accident, how can someone not seen him fall, not seen this kind of an impact if his arm was shattered like that?" said his mother, Anitra Smith.
Raleigh police said it's unlikely an assault took place, but if evidence winds up pointing to one, it would mark the second time in two years the teen was hurt while in the school system's care.
In 2006, while Jamaal was at Carnage Middle School, he was beaten by former teacher Christina Wolfe. She was convicted of assault on a handicapped person and stripped of her teachers license.
The family has a pending lawsuit in the 2006 incident.
"If someone does know something (about what happened Wednesday), please inform the principals or someone," Anitra Smith said.