Two of the boats set out from the southern province of Guangdong and sailed close to the Xisha Islands, located some 330 km (200 miles) from Hainan Island, when they were shipwrecked.
Early Monday morning, emergency management services found 13 survivors from the first two boats, after which they continued with their rescue mission.
The course the third fishing boat took is still unknown, and the number of victims could increase. Authorities said a total of five vessels with 171 people aboard have been affected by typhoon.
On Sunday China raised the alert level to orange, the second most critical after red, as the typhoon approached the coast.
Waves have reached a height of 9 metres in the western part of the South China Sea, while the roughest seas were along the Hainan coast.
Wutip is expected to make landfall on Tuesday on the central Vietnam coast after it sweeps past China.