Officials at Hamad International Airport in Doha are said to have subjected the passengers to an internal examination after a premature newborn baby was found in a bathroom.
The women complained they were told to take off all their clothes so a doctor could check whether they had given birth recently.
Channel Seven, which first reported the incident, said that 13 Australians were among the women who were forced to undergo medical examinations in an ambulance on the tarmac.
Dr Wolfgang Babeck, who was on board Flight QR908 from Doha to Sydney on 2 October, told Guardian Australia that the women "were discussing what had happened and saying that it was unacceptable and disgusting."
He said the women told him they were taken to a female doctor and “basically strip searched".
Dr Babeck added that they "had to take everything downwards off, all their clothes, even their underwear. And then the doctor would try to feel in the uterus and stomach area or lower abdomen to see whether they may have given birth recently. Someone had been told that a baby had been found in the toilet and they were trying to find out who the mother was.”
The women are believed to have complained about the incident while completing their mandatory quarantine on their return to Australia.
Australia's Department of Foreign Affairs and Trade said in a statement that the government was "aware of concerning reports regarding the treatment of female passengers, including Australian citizens, at Doha (Hamad) airport in Qatar.
"We have formally registered our serious concerns regarding the incident with Qatari authorities and have been assured that detailed and transparent information on the event will be provided soon."
Marise Payne, Australia’s foreign minister, told reporters it was a "grossly, grossly disturbing, offensive, concerning set of events”.
“It's not something that I've ever heard of occurring in my life, in any context. We have made our views very clear to the Qatari authorities on this matter," she said.
Australia will await a report from the Qatari government before “we will determine the next steps,” Ms Payne added.
She said the matter was reported to Australian Federal Police, but did not explain what action police might take. Police said in a statement they are working with the Department of Foreign Affairs and Trade on the matter and that further comment would be inappropriate.
Samantha Klintworth, the director of Amnesty International Australia, described the incident as "distressing and disturbing and it is a gross violation of these women’s human rights".
"There needs to be a thorough and independent investigation and all of those involved need to be held to account," she told Channel Seven.
Hamad International Airport (HIA) confirmed that a newborn baby had been found abandoned at the airport and “immediately provided with medical attention and care”.
The airport did not comment on reports that the women had been subjected to an intrusive examination but said that officials were trying to locate the baby’s mother.
“Medical professionals expressed concern to officials about the health and welfare of a mother who had just given birth and requested she be located prior to departing HIA,” a spokesperson told The Independent.
"Individuals who had access to the specific area of the airport where the new born infant was found were asked to assist in the query.
“At this time, the new born infant remains unidentified, but is safe under the professional care of medical and social workers. The entire team at HIA requests anyone with any information or knowledge of the mother to contact them.”