SA Police said the boy was one of three — aged 11, 12 and 13 — who were inside the bin as it was being emptied just after 5:20am.

Emergency services were called to the carpark of the Repco store, next to the drive-through of a McDonald's outlet on Liverpool Street, about 5:30am.

One of the boys managed to jump out, but the 13-year-old sustained serious injuries and died at the scene.

The third boy was not injured, police said.

Police said the three boys, all from Port Lincoln, "were allegedly asleep in an industrial bin when the bin was being emptied".

"It is believed the truck driver was unaware the boys were in the bin at the time and is extremely shaken by the incident," police said in a statement.

Police have described the boy's death as "tragic" and said a report would be prepared for the coroner.

SafeWork SA has been advised of the incident.

Port Lincoln Mayor Brad Flaherty has expressed his condolences to the victim's loved ones.

"It's a terrible, terrible incident that will have an awful impact on the community as a whole and the families involved," he said.

The area has been cordoned off, and State Emergency Service personnel are also in attendance.

Police are expected to provide more details at a media conference early this afternoon in Port Lincoln.