The incident is the third time this year that Tokyo has reported a cargo transfer by a North Korean vessel in violation of UN sanctions over Pyongyang's banned nuclear and ballistic missile programmes.
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Japan's foreign ministry said late Tuesday a military patrol plane and an escort vessel observed the apparent transfer in the East China Sea on Friday afternoon.
The Japanese navy "found the Yu Jong 2, a North Korean-flagged tanker, lying alongside a small vessel of unknown nationality... on the high sea" around 250 kilometres (155 miles) offshore from the Chinese city of Shanghai, the foreign ministry said.
Four Chinese characters reading "Min Ning De You 078" meaning "Fujian Province, Ningde City, oil tanker 078" in English, were on the small vessel, the ministry said.
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"Following a comprehensive assessment, the Government of Japan strongly suspects that they conducted ship-to-ship transfers banned" by the UN Security Council resolutions, the ministry said.
Tokyo said it had reported the incident to the UN Security Council and shared information with relevant countries.
There was no immediate indication of whether the incident had been raised formally with Beijing.
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The incident comes as global attention is focused on North Korea's participation in the ongoing Winter Olympics hosted by the South, in a diplomatic push by Kim Jong Un's isolated regime.
Pyongyang is subject to a series of UN Security Council sanctions, including one prohibiting all member states from facilitating or engaging in ship-to-ship transfers of goods to or from North Korean-flagged vessels.
The previous two incidents reported by Japan this year both involved a different North Korean tanker, the Rye Song Gang 1, one of the vessels denied international port access by the Security Council.
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