The Japanese statement said the "Chon Ma San", designated by the United States as a sanctions target, was spotted by a surveillance plane with the Maldivian-flagged tanker "Xin Yuan 18" some 250 km east of Shanghai on Saturday.
It said "Japan strongly suspects that the vessels conducted ship-to-ship transfers" banned by UN Security Council resolutions.
Maldives government denied that Xin Yuan 18 is of Maldivian origin and said "no such vessel is registered in the country."
"We condemn ... the use of our national flag in a manner so as to tarnish the good standing and reputation of our nation," the Maldives government said in a statement.
It said Maldives has prioritized the implementation of all UN Security Council resolutions including those on North Korea.
Authorities do not allow flags of convenience to foreign owned vessels to operate outside Maldivian waters, it said, adding that the government was investigating.
"The Maldives will pursue aggressive action against any such acts which affects the national identity in such a detrimental manner," it said.
The Maldives is facing a political crisis that has hurt tourism, its main revenue source and any international action could hurt its economy further, analysts say.
It is the fourth time Japan has suspected such an illegal transfer in recent weeks and comes as Washington and key Asian allies prepare to expand the interceptions of ships suspected of violating North Korean sanctions.
North Korea last year conducted dozens of missile launches and its sixth and largest nuclear test as it pursues its goal of developing a nuclear missile capable of reaching the United States, triggering deeper UN Security Council sanctions.
Washington on Friday slapped sanctions on dozens more companies and vessels linked to North Korea's shipping trade and urged the United Nations to blacklist some entities to shut down smuggling aimed at obtaining oil and selling coal.