FIBA said the suspension results from the JBA's failure to merge the 22-team Basketball Japan League and the 13-team National Basketball League, which is in violation of its general statutes.
"FIBA regrets that the situation has reached such a point of no return," FIBA secretary general Patrick Baumann 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."
FIBA's executive committee will send a representative to Japan to set up a task force that will be in charge of helping the JBA implement necessary reforms.
The ban is especially damaging for the women's team, which was in good position to qualify for the 2016 Olympics after winning its first Asian Championship title in 43 years last year.
JBA president Yasuhiko Fukatsu announced his resignation last month, saying it will be difficult for the national body to come to a conclusion on a merger between the two leagues.
FIBA did not say how long the suspension would last but Baumann said he hopes the issues will be resolved before the 2020 Tokyo Olympics.
"We want a successful Tokyo 2020 basketball tournament with the participation of the Japanese men's and women's teams," Baumann said.