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At least three people are dead and two are missing after an explosion on a refugee boat off Western Australia's northwest, police say.

Sergeant Greg Lambert said others were injured but it was not certain how many.

"It is believed an explosion has occurred in the engine compartment of a vessel," Sgt Lambert said.

"It is believed that three people have been killed, two people are missing and others are injured, numbers are not yet known," he said.

A report on said the vessel had been intercepted by a Royal Australian Navy boat near Ashmore Island yesterday.

The people on the intercepted boat were believed to be from Afghanistan.

A Royal Darwin Hospital spokeswoman was quoted in the report as saying there were 46 "casualties".

The vessel is being towed to Darwin.