Officials said heavy rain falling on the mountains surrounding Kalibo, the capital of Aklan province, caused a river running through the city to overflow and triggered a flash flood late Wednesday.
High astronomical tides also prevented the river from emptying into the sea.
Wukong arrived three weeks after Typhoon Bopha killed nearly 2,000 people in the south of the country.
Fresh memories of that disaster are credited for people taking warnings of Wukong seriously and for them evacuating low-lying areas prone to flooding.
Typhoon Wukong Track
Satellite Loop Data: CIMSS