Japan's foreign ministry said a military patrol plane observed the apparent transfer in the East China Sea early Tuesday.
"Following a comprehensive assessment, the Government of Japan strongly suspects that they conducted ship-to-ship transfers banned" by UN Security Council resolutions, the ministry said in a statement late Wednesday.
Tokyo said it had reported the incident to the Security Council and shared related information with relevant countries.
The incident involved the same North Korean tanker, the Rye Song Gang 1, that Tokyo spotted alongside a Dominica-registered oil tanker in January.
The incident comes as global attention is focused on North Korea's participation in the ongoing Winter Olympics hosted by South Korea, in a diplomatic push by Kim Jong Un's isolated regime.
Tokyo identified the Belize-flagged ship involved in Tuesday's incident as the Wan Heng 11.
The UN has imposed a series of sanctions on North Korea aimed at pressuring it to abandon its missile and nuclear programmes.
It has denied international port access to eight North Korean vessels, including the Rye Song Gang 1.
And in September, it passed sanctions prohibiting all member states from facilitating or engaging in ship-to-ship transfers of goods to or from North Korean-flagged vessels.
On Monday, Japanese Foreign Minister Taro Kono warned against countries being "blinded" by North Korea's diplomatic charm offensive at the Winter Olympics, saying the world's main goal remains ridding Pyongyang of nuclear weapons.
Prime Minister Shinzo Abe vowed to maintain "maximum pressure" on the North Korean regime following a phone call with US President Donald Trump. (AFP)