The examinations reportedly happened after staff at Hamad International Airport discovered a newborn baby in a terminal toilet.
The baby remains unidentified and is being cared for.
Thirteen Australians were among those said to have been examined.
They were taken to an ambulance on the tarmac and told to remove their underwear before being examined, Channel Seven reported.
The women were not told why they were being examined before boarding the Qatar Airways flight on 2 October.
The Australian government has raised the incident with Qatari authorities.
"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," a spokesman for the Australian Department of Foreign Affairs and Trade told local media.
A spokesman for New South Wales police, which runs the hotel quarantine operation for those arriving in Sydney, said of the incident: "Those women completed mandatory quarantine in NSW, during which time they were provided with medical and psychological support by NSW Health."
Qatar Airways have not yet responded to a request for comment.
A spokeswoman for Hamad International Airport said: "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" the airport.
The airport is seeking information about the mother, while the child is being cared for by medical and social workers.