The company is suspected of pressuring retailers to offer lower prices to compete with rival sites.
Antitrust regulators are looking into Amazon Japan's business practices.
The offices of Amazon Japan have been searched, following allegations the online retailing giant may have forced its sellers to set lower prices to compete with rival sites.
It's unclear when the raid took place. The Wall Street Journal reported on the raid Monday, following a report earlier in the day by the Nikkei business newspaper, which cited anonymous sources.
A spokesman for the Japan FTC confirmed the Nikkei's report on the raid, the Journal said.
Last year, the European Commission launched an investigation into Amazon's e-books business. Regulators there are examining whether Amazon violated competition rules when it required publishers to tell it whether they received more favorable terms from rivals.
Neither Amazon nor the Japan FTC immediately responded to a request for comment.