The ship entered a container terminal on Wednesday after officials obtained information North Korea might have loaded internationally-banned items onto the vessel, Kyodo news agency reported citing unidentified sources.
The customs officials found several containers believed to have been exported from North Korea. They contained items including aluminium rods which could be converted for military use and steel products, the report said.
The products in the containers had markings which showed that they were manufactured in the reclusive communist state, Kyodo quoted the sources as saying.
It is the first probe carried out under a cargo inspection law, which came into force in 2010 following a United Nations Security Council resolution adopted in 2009 to punish North Korea for its second nuclear test.
The law allows Japanese authorities to inspect foreign-flagged vessels suspected of carrying banned materials from or to North Korea.
The cargo ship was believed to have set sail from the northeastern Chinese city of Dalian, heading to Southeast Asian countries via Tokyo, Kyodo said.