The alleged activity took place on Monday near the remote atoll of Okinotori in the Philippine Sea roughly halfway between Taiwan and Guam. China has said it does not constitute an island.
Japan's coastguard on Monday spotted a Chinese maritime survey vessel "extending what appeared to be a wire into the waters in Japan's exclusive economic zone (EEZ) 270 kilometres east of Okinotori island," government spokesman Yoshimasa Hayashi told reporters.
"As the maritime scientific research by the vessel has not obtained Japan's agreement, the coastguard demanded that the activity stops and we lodged a protest with the Chinese side through a diplomatic channel," Hayashi said.
The Chinese vessel left the EEZ at around 10:45 pm on Monday, Hayashi said.
Under international law, a coastal state has rights to the management of natural resources and other economic activities within its EEZ, which is within 200 nautical miles, or 370 kilometres, of its coastlines.
Prior consent is necessary for foreign vessels to carry out scientific research for non-economic purposes in another country's EEZ.
However China has said Japan's claim is invalid since Okinotori, some 1,700 kilometres (1,050 miles) south of Tokyo, is just rocks and not an island.
Therefore it cannot be not regarded under the UN Convention on the Law of the Sea as an entity around which Japan can set its EEZ, Beijing has said.
Others including Taiwan and South Korea also dispute Japan's claim. In 2016 Japan briefly seized a Taiwanese fishing boat operating in the area.
Japan has in recent years invested millions of dollars in planting coral around the atoll in attempt to stop erosion by the sea.
China was yet to comment on Tuesday.
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