The comments were made by CEO Satya Nadella while he was speaking in Arizona at an event for women in computing.
Mr Nadella was asked to give his advice to women who are uncomfortable requesting a salary raise.
He replied that women should have faith that the system will give them the right raises as they go along.
"It's not really about asking for the raise, but knowing and having faith that the system will actually give you the right raises as you go along," Mr Nadella told the Grace Hopper Celebration of Women in Computing.
"Because that's good karma... It'll come back because somebody's going to know that's the kind of person that I want to trust."
The comments by India-born Mr Nadella, who has a remuneration package of around $7m (£4.3m), sparked a torrent of criticism on social media.
"Truly horrified that Satya Nadella could tell women at Grace Hopper not to ask for raises," tweeted Julie Bort.
"Wow Microsoft, That's a new low for you," Isik Mater tweeted in response.
"I'll wait for Karma to lower my #xboxlive price too," tweeted Chuck Granade.
"Was inarticulate re how women should ask for raise," he tweeted.
"Our industry must close gender pay gap so a raise is not needed because of a bias."
Microsoft also posted an all-staff memo from the CEO on its website.
In it, Mr Nadella said he answered the question posed by interviewee Maria Klawe "completely wrong".
"Without a doubt I wholeheartedly support programmes at Microsoft and in the industry that bring more women into technology and close the pay gap," Mr Nadella wrote.
"I believe men and women should get equal pay for equal work.
"And when it comes to career advice on getting a raise when you think it’s deserved, Maria's advice was the right advice. If you think you deserve a raise, you should just ask."
Mr Nadella's remarks at the Grace Hopper conference have the potential to harm both sales of Microsoft products and the appeal for female tech workers in Silicon Valley to work for the IT giant.
Of more than 100,000 employees at Microsoft, only 29% are female, according to data released by the firm recently.
The controversy comes just days after reports of the deteriorating relationship between Microsoft founder Bill Gates and its former CEO Steve Ballmer.