FIBA wants a single league in Japan, arguing that disagreements between the bj-league and the National Basketball League (NBL) have affected the growth of the sport in the country.
The governing body's secretary-general Patrick Baumann said Japan had until Oct. 31 to find a solution but denied reports that failure to do so would have consequences for the 2020 Games.
"Those stories are not true at all, I never said that. We want to see an end to the problem and they have to make changes," Baumann told Reuters in Barcelona.
"The deadline will be October 31st for them to do this and then we will see what happens but they will not be prevented from playing in 2020, that is not something we are planning."
Akihiro Ejima, a spokesman for the bj-league in Tokyo, said nothing concrete has been decided but the two sides have finally agreed on the points of discussion.
"The deadline is important, but the last thing we want is to rush and end up forming an unsustainable pro league, so we are handling this very carefully," he added.
The NBL had no immediate comment.
Japan's men have appeared at the Olympics six times but never since Montreal 1976 and basketball lags a long way behind soccer and baseball in terms of fan participation, ticket sales and television revenue.
Average attendance per game is about 1,800 for the bj-league and around 1,300 for the NBL, and games are rarely televised on national television.
The bj-league broke away from the then-Japan Basketball League in 2005 with bright hopes of creating Japan's first professional championship. It was recognised in 2010 by the Japan Basketball Association.
The NBL was founded last year and is a corporately run league.
(Additional reporting by Megumi Lim in Tokyo; Editing by Alan Baldwin and Julian Linden)
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