"Ray Moore's comments towards women's tennis were disparaging and made in poor taste, as Ray has subsequently acknowledged," ATP Executive Chairman and President Chris Kermode said in a statement on Monday.
Kermode also said the ATP, the governing body for men's tennis, supports equality across society but acknowledged that it operates in the sports and entertainment business.
"The ATP seeks to achieve fair compensation for its players by setting minimum prize money levels for ATP events in accordance with the revenues that are generated from men's professional tennis," said Kermode.
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"The ATP also respects the right of tournaments to make their own decisions relating to prize money for women's tennis, which is run as a separate Tour."
Men and women's players receive equal prize money at each of the year's four grand slam tournaments, some $75 million, where both genders share the spotlight.
Total prize money on the ATP Tour is about $188 million, while the women's WTA Tour (Women's Tennis Association) is roughly $130 million.
Moore, a 69-year-old South African and former ATP Tour player, also singled out Canada's Eugenie Bouchard and Spaniard Garbine Muguruza as being among the "very attractive prospects" on the WTA circuit tour, before explaining that they were "physically attractive and competitively attractive."
Added Moore: "If I was a lady player, I'd go down every night on my knees and thank God that Roger Federer and Rafa Nadal were born, because they have carried this sport."
His comments drew wide scorn and even prompted tennis great Martina Navratilova to say she would not be surprised if female players boycotted the tournament at Indian Wells as long as Moore was in charge.
"It was really disheartening to see Ray Moore offer the extremely prejudiced and very old fashioned statements regarding women tennis players," said Navratilova.
"We have made it this far on our own, without help from male players, and will continue to do so in the future.
"It would be hard to imagine any women to want to go and play at Indian Wells if Moore stays as the tournament director."
(Reporting by Larry Fine in New York; Additional reporting by Martyn Herman in London; Editing by Frank Pingue)
