Among the hardest hit cities was Hue, Vietnam's old imperial capital, where 16,000 homes have been partially submerged, according to the National Steering Committee for Natural Disaster Prevention and Control.
State media reported that a 40-year-old woman died and her 18-year-old daughter was missing after they were swept away by floodwaters when a boat they were travelling in capsized at the world heritage site.
In Quang Tri province, the body of a 36-year-old man who had gone fishing on a lake was found Wednesday, state media added.
Across five central provinces, more than 4,000 people have been evacuated from their homes, authorities said.
Parts of the national highway linking north and south Vietnam have also been blocked by landslides due to the flooding.
The country is frequently lashed by harsh weather in the rainy season between June and November.
Forecasters said the rain will continue in the area for another day before improving this weekend.
According to official figures, natural disasters including floods and landslides have left 138 people dead and missing in Vietnam this year.
Scientists have warned extreme weather events globally are becoming more intense and frequent due to climate change.
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