The boat was seized on Saturday near Japan’s Kagoshima Prefecture, China’s Xinhua news agency reported, citing the Chinese consulate in Fukuoka, Japan.
The captain had admitted entering Japanese waters, Xinhua said.
The incident comes months after anti-Japanese protests in Chinese cities over disputed islands near Taiwan.
The captain and two crew members have been taken to Kagoshima for questioning while six other sailors remained on board the boat, which comes from Fujian province in south-east China, Xinhua said.
A Chinese consulate official has been sent to Kagoshima to visit the crew members, the report added.
Relations between Japan and China have been strained over the disputed islands, known as the Diaoyu in Chinese and Senkaku in Japanese.
Japan controls the islands, which are also claimed by Taiwan. Close to strategically important shipping lanes, the waters around the islands also offer rich fishing grounds and are thought to contain oil deposits.
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