The Gulf carrier has a close business partnership with British Airways and is also the largest single shareholder in BA's parent company, IAG.
Al-Baker is the new chairman of the board of governors of IATA, where only six of its 280 members have female chief executives, BBC reports.
Al Baker tried to diminish the scope of his comments.
"I look forward to continuing my work in the coming year for a transparent and fair aviation industry the world over, a sector which will only continue to grow in the years ahead, and one in which I am most proud to work and represent the World's Best Airline", he added. "I used to be not referring to the employees usually".
When asked about gender inequality at airlines in the Middle East, he retorted: "not in Qatar Airways".
Alan Joyce, chief executive of Qantas, said 40 per cent of the airline's senior management is female, including the head of worldwide business, noting that an airline not tapping female talent will be "disadvantaged".
As the official airline partner of the global shipping exhibition, Posidonia 2018, Qatar Airways is participating in the biennial event, which is taking place until June 8, at the Metropolitan Expo in Athens.
In 2014, Qatar Airways defended policies on pregnancy and marriage for cabin crew after coming under fire over working conditions in the conservative Gulf emirate.
On Wednesday, Al Baker apologised, saying his remarks had been intended as a joke and had been taken out of context.
Past year he derided USA airline companies for having "grandmother" flight attendants, and boasted that the average age of his flight crew was 26.
In fact, during the same IATA press conference, where he made his sexist remarks, the airline's executive promised to abstain from his controversial style, whilst chairing the organization.
Alan Joyce, the gay chief executive of Qantas Airways who campaigned for marriage equality in Australia, had sat next to Mr Baker at a session on the topic. "He lasted 10 minutes - 10 minutes", Mr Joyce said.
"I suspect the woman running Germany, for instance, could probably cope with Qatar Airways", said Sam Freedman, the Executive Director at Teach First.
"Aer Lingus recruited its first female pilot in 1977..."
But he said it was "going to take a long time to fix some of the issues that are inherent in our society", such as girls not studying science and technology in schools, which impacted their numbers in engineering and flying roles.
"To be nominated to such a prestigious leadership position in the industry is a great honour, made all the more pertinent in the hard circumstances in which Qatar Airways now operates".