The boat, which belongs to Fujian Province in southeast China, was seized yesterday near Japan's Kagoshima Prefecture with Lin Shiqin, the captain, and eight crew members aboard, state-run Xinhua news agency reported today.
Lin and the crew members all are Chinese nationals, the Chinese Consulate General said.
The captain, who admitted that his boat had entered Japanese waters, and two crew members have been transferred to Kagoshima for questioning.
The other sailors remained aboard the boat in waters where it was seized, the report said.
The Chinese Consulate General has sent a consul to Kagoshima to visit the crew members and has asked Japan to ensure their safety and legitimate rights, it said.
The seizure of the Chinese boat comes in the midst of China-Japan tensions over their claims on islands in the East China Sea.
Ships from both the countries are aggressively patrolling the islands called Senkakus by Japan and Diaoyu by China to claim their ownership.