Three boys, aged 11, 12 and 13, were asleep as the bin was being routinely collected in Port Lincoln early on Tuesday morning.

The 12-year-old scrambled out and started "banging" on the cabin door to alert the truck driver, but it was too late to stop the skip tipping.

The teen sustained serious injuries and died at the scene, while the younger boy was unharmed.

Superintendent Paul Bahr said police had spoken with the "traumatised" surviving pair but had not been able to establish why they were sleeping in the bin.

"It's tragic across a whole number of levels," he told reporters on Tuesday.

"And that's just one of the levels of the tragedy of this as to why these three children thought they needed to be sleeping in the bin.

"On what was a pretty cold and wet night, too. It wasn't a good night to be sleeping outdoors."

He said the boys, who are not believed to be related, had beds they could have slept in.

"It's fair to say that the boys had somewhere to stay," Supt Bahr said.

"I don't think it'd be fair to classify them as homeless."

The truck driver was taken to hospital for assessment and is understood to be extremely shaken.

Supt Bahr said police had not previously been aware of reports of kids sleeping in Port Lincoln bins.

"Port Lincoln has an issue with homelessness like every community, and from time to time we do get rough sleepers," he said.

"I'm not aware of children sleeping rough."

Port Lincoln Mayor Brad Flaherty said the council was "deeply saddened" by the incident.

"This is devastating news for the community and those family and friends who are directly impacted," he said.

Safe Work SA has been advised and police are preparing a report for the coroner.

Australian Associated Press