Yuriko Koike urged the private country club on January 13 to let women play golf on any day of the week after women had only been allowed to golf Monday through Saturday if they were accompanied by a male member.
The Tokyo 2020 Olympic golf venue has voted to admit women as full members.
"We are pleased to learn that the Kasumigaseki Country Club voted today at an extraordinary meeting of its Executive Board to amend the club's membership policy in keeping with the spirit of the Olympic Charter", he said.
The change means organisers won't have to find a different golf venue.
The Tokyo 2020 golf venue had faced the potential removal of its hosting rights after the International Olympic Committee said it would only go to a club with a non-discriminatory policy.
Kasumigaseki CC was founded in 1929 and has hosted more high-level tournaments in Japan than any other course, including the 1999 Japan Ladies Open and 2010 Asian Amateur Championship which was won by Hideki Matsuyama.
"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".
"We will continue to make our very best efforts to prepare for and deliver a successful Tokyo 2020 Games".
The historic Muirfield Golf Club in Scotland, which has hosted the British Open 16 times since 1892, voted to allow its first female members in its 273-year history on Friday after the tournament's governing committee announced that the club wouldn't be allowed to host anymore tournaments if they didn't let women to join.
The Royal and Ancient (R&A), who organise The Open Championship, had axed Muirfield from their list of venues after members at the club made a decision to uphold their rules on not allowing women to join.
International Olympic Committee vice-president John Coates told the BBC earlier this month before the vote, "I respect it's a private club but our position is clear".
The club's board met February 7 to discuss the matter and then held three meetings with full members to explain the situation and hear their views.