A Department of Foreign Affairs and Trade spokesman confirmed the tragedy on Saturday evening, stressing that the distraught family had asked for privacy.
"We confirm the death in Bali of a 54-year-old woman and her 14-year-old daughter from Queensland," he told AAP.
"Our condolences are with the family and the family have asked that their privacy be respected during this difficult time."
Police sources have told AAP the mother, a Sunshine Coast health professional, and her teenage daughter checked in to their beachfront resort on Bali's east coast on Friday.
Early on Saturday morning the girl asked staff at the Padang Bai Beach Resort for help, telling them she and her mother had fallen sick.
The pair were taken by private ambulance to a nearby medical centre but about 1.45am local time the mother died, according to local sources.
The girl was rushed to BIMC Hospital, an international clinic in the Balinese capital of Denpasar, but could not be saved.
The bodies are now at Sanglah Hospital awaiting autopsy, one police source said.
"Checking the scene, we found lots of medicine," he told AAP.
"We can't confirm the cause of death yet."
Another senior local police source has told AAP the treating doctor at the first clinic suspected a food allergy.
"What kind of food, we don't know," he said.
"All the medicines are from abroad.
"The vomit and medicines have been taken to forensic laboratory."
DFAT says the Australian Consulate-General in Bali is liaising with local authorities and the government is providing consular assistance to the family in Australia.
