"I was not referring to the staff in general", he said.
Mr Al Baker responded by saying that "it's not in Qatar Airways".
He later said Qatar Airways was the first carrier in the region to have female pilots and the company had women in senior roles.
He went on to list the efforts Qatar Airways has made toward gender equality, noting that more than 33 percent of the airline's employees are women and it was the first airline in the Middle East to introduce female pilots.
Though Al Baker's remarks prompted disapproval during the news conference, he's far from the first senior executive to find himself under fire for such statements.
Al Baker's elevation to Iata chair comes seven years after he launched a ferocious attack on the organisation's leadership at the annual meeting, and four years after he hosted a sumptuous AGM in Qatar, surprising airline executives with a guest appearance by Kylie Minogue after the evening meal.
Moments after becoming chairman of the International Air Transport Association's board of governors, one of the world's biggest boys' clubs, Al Baker did little to suggest things will change. SkyTeam appointed Delta executive Kristin Colvile as chief executive of the airline alliance earlier this month.
'Solo: A Star Wars Story' could lose $50M for Disney
The survival tale is based on a true story and scored 67 percent positive reviews, according to aggregator Rotten Tomatoes. STX Entertainment's " Adrift " collected $11.5 million against a forecast of $13 million and budget of $35 million.
Mr Baker also said that he would welcome a female leader, providing he could train her up.
Promises by the global airline industry to do more to promote gender equality veered off course when one of its top executives suggested his CEO role was too hard for a woman. We see that they have huge potential in doing senior management positions.
"I was only referring to one individual", he said.
Al Baker added that "it will be my pleasure to have a CEO candidate I could develop to become CEO after me".
"But there's a degree of optimism in our ability to handle it, we're stronger than we were a few years ago as an industry".
USA and some European airlines have accused Gulf carriers of unfair competition based on subsidies and social policies, but Walsh - whose group counts Qatar Airways as a shareholder - said he believed Gulf airlines competed on an equal footing.
Cathay CEO Rupert Hogg said there were no immediate vacancies on the top team but there were women managers a level below and diversity was valued at the airline, which has staff from 75 nationalities and is a supporter of the Gay Games 2022 in Hong Kong. "It's taken 40 years to get to 10%", he said.