Indonesian police have confirmed an Australian woman has been robbed and raped at knifepoint in Bali.

The 28-year-old Perth woman was on holiday with her family at the time.

She told Bali police that a man carrying a knife and torch appeared in the room of her Kuta villa about 4am on Saturday.

The man forced her to show him where her valuables were and took three iPads, two mobile phones and cash.

He then told her to take off her clothes before raping her.

The chief of North Kuta Police, Captain Reinhard Nainggolan, says a doctor has confirmed signs of sexual assault.

Indonesian police are investigating and say there may have been other people involved in breaking into into the complex, but there is only one suspected rapist.

The woman and her family ended their holiday early and have now returned to Australia.

Earlier this year intruders at a Bali villa attacked and stabbed an Australian man, and three other Australians have died in Bali since December.