The mandatory detention of illegal immigrants should end, Amnesty International said yesterday after two men escaped from South Australia's Woomera Detention Centre.

The human-rights watchdog said asylum seekers should be kept in community centres, not jailed.

Two refugees who escaped from Woomera in SA's central desert were found in Port Augusta yesterday and are expected to face charges.

An Immigration Department spokesman said an investigation into the incident was underway.

"They're expected to face charges relating to escaping from immigration detention," the spokesman said.

The men, believed to be in their 20s, allegedly fled from the Woomera centre about midnight on Monday amid a protest involving some of the 1300 people being held there.

Amnesty International's National Refugee Coordinator Des Hogan said it would be cheaper and more humane to keep refugees in community centres.