It found the French bank guilty of breaching Japanese securities regulations amid allegations that one of its traders had attempted to manipulate a share price.
The FSA explained that the suspension related to what it described as a "massive" order to buy stock in November 2008.
It also said BNP Paribas's internal controls were insufficient to prevent the attempt by the trader to manipulate the value of the stock.
Press reports in Japan suggested the stock in question was mobile phone company Softbank Corp, but the FSA would not confirm the rumors.
The suspension, which comes less than a year after Japanese regulators ordered BNP Paribas to tighten its internal controls, will be served during the opening two weeks of November.
BNP Paribas's Japanese operation did have some better news earlier this month when it was named Best Derivatives House in The Asset magazine's Triple A Investment Awards.
Written by Asim Shah