Amazon Japan said its offices have been raided by the country's fair trade regulator on suspicion of anti-trust violations.
The online retailer is suspected of asking suppliers to shoulder costs incurred for selling their products at a discount, according to media reports.
The firm said it is cooperating with the investigation by Japan's Fair Trade Commission (JTFC), Reuters reported.
JTFC declined to provide more details on the case when contacted by the BBC.
It's not the first time Amazon Japan has been investigated over anti-trust breaches.
In 2016, JTFC raided the firm's offices on suspicions it had unfairly forced retailers to set prices on Amazon Japan as low or lower than prices for those products listed on other e-commerce sites.
Regulators ended the investigation in June last year when Amazon Japan agreed to stop the practice.