The private Kasumigaseki Country Club in Saitama prefecture, which is set to host both men's and women's tournaments in July and August 2020, forbids women from playing on Sundays and excludes them from becoming full members.
Coates, who is head of the coordination commission which oversees preparations for the Games, said he had only become aware of the issue on his last visit to Tokyo at the end of last year and that organisers were now aware of the IOC's stance.
"We made quite clear that there has to be gender equality," Coates said in an interview at the Asian Winter Games in the northern city of Sapporo.
"If they can't achieve the gender equality then we have to get another course, but the organisers are very confident that they will."
Japanese media reported that members of the club had met on Sunday to hear an explanation of the situation. The club was closed on Monday and nobody was available to comment.
Coates said he was aware that discussions were underway.
"They either will or they won't," he said. "There's plenty of time to move to another golf course if we have to."
Tokyo 2020 organisers unveiled a revised budget of $US16.8 billion ($21.86 billion) in December and vowed to seek further savings in cooperation with the IOC.
Coates said the budget issue should be resolved some time this year and the final figure would be nowhere near the 3.0 trillion yen ($34.5 billion) that a Tokyo city government panel forecast last year.
"The costs that were being speculated were vastly over-speculated," he said.
"We haven't yet accepted a final budget. (It should be worked out) on this forthcoming visit or the one after."
Coates first became widely known in international sport when he helped Sydney first win the bid for the 2000 Olympics and then deliver the Games, at which the South and North Korea teams first marched together at an opening ceremony.
A North Korean missile test and the murder in Malaysia of the half-brother of the country's leader have heightened tensions in the peninsula less than a year before the South hosts the Winter Olympics.
The IOC member for North Korea said at the weekend that Pyongyang would send athletes to Pyeongchang and Coates saw no reason to doubt him, even if he thought it unlikely the two teams would again march together at the opening ceremony.
"That's a matter between the two national Olympic committees," he said. "If it happens, that's nice but I can also understand that at a home games, I would think that the host would want march on their own, I'm sure they would."