Baker stirred negative headlines for the Gulf carrier with his sexist remark at the International Air Transport Association's (IATA) two-day annual meeting in Sydney.
But on Wednesday a contrite Baker said sorry while also lashing out at the coverage, in a statement issued by the Doha-based airline.
"I would like to offer my heartfelt apologies for any offence caused by my comment yesterday, which runs counter to my track record of expanding the role of women in leadership throughout the Qatar Airways Group and has been sensationalised by the media," he said.
On Tuesday at the IATA meeting, asked why Qatar Airways was led by a man, he replied: "Of course it had to be led by a man because it is a very challenging position."
His comments, which he also put down to his sense of humour, drew groans from assembled journalists, according to media reports.
Baker was appointed chairman of IATA during the meeting, where gender parity was one of the major issues.
IATA currently has just two female CEOs on its 31-member board, and figures it released in March showed three percent of CEOs in the airline industry were female, compared with 12 percent in other sectors.
Baker is well-known for being outspoken.
In March 2015, he accused US rival airline Delta of flying "crap" planes. And he had to apologise last year for calling female American flight attendants "grandmothers".
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)