The boy was found on Thursday afternoon on Holme Station Bridge, about 15 km west of Timaru.
Police would not disclose the exact nature of his injuries but it is understood there was a significant amount of blood on his Oceanview Heights school uniform.
Police appealed to the public for information.
"Even if you don't believe you saw anything we are still wanting to know who and what vehicles were in the area during that time," police said.
The boy was described as having a dark complexion, of slim build, about 30kg with dark hair. While he was 9, he was considered small for his age and his height was more like that of a 6- or 7-year-old.
Anyone with information was urged to contact Timaru police.