FIBA announced on Wednesday that the JBA would no longer be able to compete in international competitions, including the Olympic Games, following the conclusion of a two-day Executive Committee meeting.
The governing body had requested a restructure of the association, while also asking for changes to the domestic basketball league.
Japan's women were in with a chance of qualifying for Rio 2016, while Tokyo will host the Olympics in 2020.
"FIBA regrets that the situation has reached such a point of no return," the governing body said in a statement.
"However, we are convinced that after so many years of warnings and struggle, and for the good of basketball in Japan, it is absolutely time to make important changes to the structures of the JBA and of the domestic competitions in order to fully comply with FIBA's General Statutes and also to embrace the opportunity that the 2020 Olympic Games will provide to basketball in Japan.
"We want a successful Tokyo 2020 basketball tournament with the participation of the Japanese men's and women's national teams."