Invasive body examinations of a group of Australian women provided the "context" for the decision to deny Qatar Airways' request for extra flights.
Transport Minister Catherine King has faced intense questioning over why she rejected a bid by the airline to double the 28 weekly services it currently offers.
Thirteen Australian women were detained at Doha's Hamad International Airport in October 2020, after a baby was found abandoned in a bathroom.
Qatari authorities were searching for the mother, before they pulled women off several flights who were then led away without explanation, and ordered to strip down so they could be examined for signs of childbirth.
Five women are taking legal action.
Asked if the poor treatment was behind her choice, Ms King replied: "It was the context of the decision that I made."
Ms King said there was no "one factor" she would point to that swayed her decision "one way or the other".
"In making this decision I did have a national interest, not commercial interests, at play when I was making that decision," she said.
In July, Ms King denied the incident was the reason the airline's request for greater access was rejected.
The transport minister confirmed she had consulted with ministerial colleagues and considered stakeholder views.
Ms King said she made her decision on July 10, and told Prime Minister Anthony Albanese before it was made public on July 18.
Repeatedly questioned in parliament about the specific date Mr Albanese was informed, the transport minister would not confirm it.
"I informed the prime minister prior to my decision being made public, and normally these decisions are not made public," Ms King said.
"For context, my office had received multiple media requests about the women."
Asked if he had confidence in the transport minister, Mr Albanese, who is in Indonesia, replied: "Of course I do."
Trade Minister Don Farrell said he couldn't "specifically" say if he had a conversation with the minister.
The coalition has accused the government of protecting Qantas from competition by denying Qatar Airway's application for extra flights into Australian international airports.
Opposition Leader Peter Dutton said the government was not giving transparent answers, and he attempted to have the lower house express concern at the "sweetheart deal" with Qantas.
"The minister for transport ... has failed to give any clear or consistent explanation for this decision, has offered up to nine different explanations," he said.
A Senate committee looking into the decision is expected to invite submissions from past and present Qantas chief executives, other airlines, airports, economists, the Qatari ambassador, the consumer watchdog and the Productivity Commission.
Mr Dutton said there was a moral imperative for former Qantas boss Alan Joyce to front the inquiry, which will report by October.
The government has resisted calls for the decision to be reviewed.