The airline pointed to a Bloomberg News interview in which he said he had not meant to refer to all women at the company.
In an interview with Bloomberg, Al Baker clarified his statement, explaining that he was referring to "one individual".
An IATA board photograph published last week featured one woman out of 26 airline chiefs - Christine Ourmières-Widener, chief executive of United Kingdom regional carrier Flybe.Other airline companies have made efforts to promote women to senior positions in recent years.
"Well, of course, it has to be led by a man, because it is a very challenging position", Mr Al Baker said.
Mr Al Baker rattled those attending a press conference on Tuesday when he claimed only a man could handle the challenges of leading Qatar Airways.
He said Qatar Airways was the first carrier in the Middle East to have female pilots and that the company had women in senior roles.
"When you have diversity, your company's results are better", she told Reuters earlier on the sidelines of the Sydney airline talks. "Because it is a very challenging position", Al Baker responded, prompting gasps and groans from the room of reporters.
This is not the first time that the Qatari CEO, who is also the non-executive director of Heathrow Airport Holdings, has caused a public outcry. "As a matter of fact (at) Air Italy the majority shareholder has shortlisted women to be CEO and as minority shareholder we are actively encouraging that".
Qantas' chief said at the same press conference that the Australian carrier had achieved a strong turnaround in profits partly due to its pursuit of diversity, with women making up 40 per cent of senior management.
US 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.
"It will be my pleasure to have a female CEO candidate I could then develop to become CEO after me", he concluded.
"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". The theme of gender imbalance was a major topic of discussion at the 74th edition of the IATA annual general meeting this year, in which a majority-male group of executives agreed that more needed to be done to get more women in senior management roles at airlines.