Then, in a statement released by the airline, Al Baker portrayed his initial comments as a joke, saying he is known for "some lightheartedness at press conferences".
Qatar Airways CEO is backtracking on comments he made on Tuesday, insinuating that women could not run the airline.
Willie Walsh, CEO of British Airways and Aer Lingus owner IAG ICAG.L , said the industry needed to attract more women and that progress had been slow.
The 56-year-old CEO told journalists that women were not being underrepresented at the airline, adding: "Of course it has to be led by a man, because it is a very challenging position", he said, prompting boos from audience members.
"What are some of the resolutions, some of the ideas, that IATA will try to bring to the forefront, to have more women represented in airlines?" the reporter asked.
It's not the first time that the Qatar Airways boss has sparked controversy.
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Mr Al Baker's response was met with gasps, boos, and indignant responses from the media, with Qantas chief executive Alan Joyce reminding Mr Al Baker of his promise to refrain from making controversial comments after accepting his position as chairman of the IATA board of governors.
'So we actually encourage women. He was named Qatar Airways' Group chief executive in 1997.
Al Baker added that "it will be my pleasure to have a CEO candidate I could develop to become CEO after me".
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.
Mr Joyce said that having a diverse workforce could help drive profits.
"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".
"Aer Lingus recruited its first female pilot in 1977..." It's taken 40 years to get to 10 percent, ' he said at the CAPA-Centre for Aviation summit also taking place in Sydney.