The Saitama prefecture venue is scheduled to host both men's and women's tournaments in July and August 2020 but rules forbidding women from both playing on Sundays or becoming full members had been roundly condemned, leading to Monday's vote.
"We are pleased to learn that the Kasumigaseki Country Club voted today... to amend the club's membership policy in keeping with the spirit of the Olympic Charter," Tokyo Games chief Yoshiro Mori said in a statement.
"On behalf of the Tokyo 2020 Organising Committee, I'd like to extend my gratitude to the members of the club for their understanding and cooperation.
"I also would like to express my admiration for the club's endeavour to come to an agreement in such a short period of time."
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The club was closed due to a national holiday on Monday, meaning no one was available for comment when contacted by Reuters.
IOC vice president John Coates had last month said that organisers would seek an alternative venue if the club could not achieve gender equality and Olympic chief Thomas Bach reiterated the governing body's stance last week.
"Kasumigaseki Country Club is an outstanding venue with excellent courses, and we are proud it will be hosting world's top-tier golfers from all over the world for the Olympics Games," Mori added of the decision.
"I truly appreciate the numerous efforts that the club's senior leaderships and all the club members have made so far to meet the requirements for hosting Olympic competitions."
Several notable golf clubs have changed their policies to allow female members in recent years.
In 2014, the Royal and Ancient Golf Club of St Andrews decided to allow women to join following 260 years of exclusion, after Augusta National, home of the U.S. Masters, had ended its men-only membership two years earlier.
Last week, Muirfield voted to admit women members, scrapping a policy that led to the historic Scottish links course being stripped of its eligibility to host the British Open.
(Reporting by Simon Jennings in Bengaluru; Editing by John O'Brien)
