The boats sank Sunday near the Xisha Islands off China, Xinhua reported.
Fourteen survivors had been rescued.
Xi ordered local authorities to carry out an "all-out rescue effort," the report said.
Premier Li Keqiang made similar demands and asked local authorities to take precautions to ensure the rescuers' safety.
The boats that sank when caught in Typhoon Wutip were from Guangdong province in southern China.
China's maritime officials raised the wave warning from yellow to orange, the second-highest of the country's four-tier, color-coded weather warning system, as the storm approached land.
Waves up to 30 feet high were expected in the western South China Sea.
The National Marine Environmental Forecasting Center said storm tides were expected in Guangdong, Hainan and Guangxi provinces.
Wutip, the 21st typhoon of the season, is expected to make landfall on Vietnam's central coast Tuesday, Xinhua said.