The provincial committee for flood and storm control said six deaths were confirmed in Song Cau town and five in Tuy An district.
A total of 140 houses collapsed, 1,899 others were damaged, more than 625 hectares of rice and subsidiary crops were destroyed and 16 boats sank.
Flooding also disrupted traffic on National Highway No1A running across Chi Thanh town and An Dan commune in Tuy An district and Xuan Loc commune in Song Cau district.
Landslides brought north-south trains to a halt, leaving thousands of passengers stranded in Khanh Hoa and Binh Dinh provinces.
Heavy downpours and rising flood waters hampered rescue work in low-lying areas. Many communes in Tuy An and Dong Xuan districts and Song Cau town were submerged and cut off. In Tuy An district alone, at least 3,000 houses were two to three metres under water.
Eight motorised boats were called in to rescue the victims, but could not reach the isolated houses.
Dao Tan Loc, Secretary of the provincial Party Committee, said that the Ba Ha River hydro-electric power plant is opening its flood gates which could cause massive flooding in the downstream area. Rescue workers are working around the clock to evacuate people from danger areas to safer zones.
The government has agreed to send its helicopters to support rescue work, but the bad weather makes it impossible for them to reach the flooded villages.
Minister of Agriculture and Rural Development Cao Duc Phat is in Phu Yen to rescue work.