Bali's police chief said the victim, Paul Gill, 42, underwent surgery at Bali International Medical Center Hospital and is being treated for stab wounds on his neck, shoulder and face.
Family friends said he is in critical condition.
The Australian Broadcasting Corp. said Gill, who moved to Indonesia six months ago, confronted a burglar who was trying to steal things from his children's room.
The incident occurred at 2 a.m. Friday.
The Jakarta Globe said the robbers escaped but it's not clear whether they were able to steal anything.
Police said they are investigating the incident and interviewing witnesses.