The women were then examined for signs they had recently given birth.
"(Officials) were forcing women to undergo invasive body searches - basically forced pap smears," a source in Doha briefed on the incident told AFP, referring to an internal examination of the cervix.
The incident, first reported by Seven News, happened on 2 October and came to light after a number of affected Australian passengers spoke out.
“This is a grossly, grossly disturbing, offensive, concerning set of events. It is not something that I have ever heard of occurring in my life, in any context,” Senator Payne told reporters in Canberra on Monday.
She said the government has been liaising directly with Qatari authorities in both Doha and Australia, and is expecting to receive a report on the matter later this week.
“I want to see the report of what occurred at the airport and I understand that the Qatari authorities intended to make that available. Once I have seen that we will determine the next steps,” she said.
Seven News said the baby had died, but a statement from the airport said while the mother of the baby has not been located the baby itself was safe.
Marise Payne slams Qatari airport invasive searches of women
"At this time, the newborn infant remains unidentified, but is safe under the professional care of medical and social workers," the statement read.
One of the flights involved, Qatar Airways' 2 October flight QR908 to Sydney, was four hours late departing Doha as a result of the incident, according to specialised air traffic website Flightradar24.
Women from several other countries and flights are understood to have been affected, but the extent of the incident is not yet known.
Earlier on Monday, the Department of Foreign Affairs and Trade said it had received advice the women were not in a position to have given consent to the searches.
“The advice that has been provided indicates that the treatment of the women concerned was offensive, grossly inappropriate, and beyond circumstances in which the women could give free and informed consent,” DFAT said in a statement.
Senator Payne said officials have been in contact with the Australians involved and have been giving them "appropriate support", including mental health support.
Opposition leader Anthony Albanese said the reports were extremely disturbing.
"The idea that women could be subject to these very intrusive searches is in my view an absolute disgrace. Our hearts go out to the women impacted by this," he said.
Nationals MP Barnaby Joyce also said it was outrageous and completely unacceptable the women were subjected to such humiliating examinations.
Qatar Airways has been contacted for comment.
Qatar practices a strict form of Islamic law, with stiff penalties applied to women who fall pregnant or bear children outside of marriage.
The coronavirus pandemic has grounded many airlines' long-haul operations, including those of Australia's flag-carrier Qantas, while Qatar Airways has continued to fly many of its routes despite the downturn in demand.
Additional reporting by AFP, AAP.