Thirteen Australian women were strip searched in Doha earlier this month.
Authorities pulled the women off a plane after a baby was found in a bathroom.
They said they were told to remove their underwear and they were examined.
The federal government has registered a complaint with Qatari authorities.
The baby has been confirmed to be alive and is being cared for by social workers.
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Thirteen Australian women were forced to remove their underwear for an invasive medical examination on the runway at Qatar Airport after a premature baby was found in a terminal bathroom.
The baby was found alive at the Hamad International Airport in Doha earlier this month and a flight to Sydney was held up while officials tried to work out who the baby belonged to.
Passengers say all the women on board, including 13 Aussies, were detained and forced to have an invasive medical examination in an ambulance on the tarmac.
The mother was not found and the women were allowed to depart before serving hotel quarantine in Sydney.
Wolfgang Babeck, who was on the flight, told the ABC that many of the women were distressed when they returned to the plane.
'When the women came back, many of them or probably all of them were upset - one of them was in tears, a younger woman,' he told the ABC.
'People couldn't believe what had happened.'
A source in Doha briefed on the incident said: '(Officials) were forcing women to undergo invasive body searches - basically forced Pap smears.'
Foreign Minister Marise Payne has expressed 'serious concerns' to Qatari officials and is awaiting a report to find out exactly what happened.
She said the events were 'grossly disturbing, offensive and deeply concerning'.
It is understood none of the women were told about the abandoned baby prior to the humiliating physical examination.
Hamad International Airport management said the baby was safe and being cared for by medical and social workers.
Medical professionals were concerned for the mother's health after the infant was found and had requested she be located.
'Individuals who had access to a specific area of the airport where the newborn infant was found were asked to assist in the query,' airport management told the ABC.
An Australian federal government spokesperson said the treatment of the women was offensive, grossly inappropriate and beyond circumstances in which they could give free and informed consent.
'The Australian government is deeply concerned at the unacceptable treatment of some female passengers on a recent Qatar Airways flight at Doha Airport,' the spokesman said.
'The government has formally registered our serious concerns about this incident with Qatari authorities. The Department of Foreign Affairs and Trade is engaged on this matter through diplomatic channels.'
The women complained about the incident while in hotel quarantine after returning to Australia.