The distant-water fishing vessel "Lupeng Yuanyu 028", owned by Penglai Jinglu Fishery Co Ltd based in Shandong province, capsized early on Tuesday, state-run CCTV reported.
The 39 people on board - 17 Chinese crew members, 17 Indonesians and five from the Philippines - were missing, CCTV said.
Xi said all efforts should be made for the rescue and early warning alerts of safety risks would be strengthened for distant-sea operations, CCTV reported.
China's maritime search and rescue center had informed relevant countries of the accident and the foreign ministry had told its missions in Australia, Sri Lanka, Maldives, Indonesia, the Philippines and other countries to coordinate search and rescue operations, it said.