Access to several communities in central Ha Tinh province has been cut off, while the police and military have been mobilised to rescue people from high-risk areas.
A woman and a 13-year-old boy were found dead in the province after being swept away by strong currents.
A search for a 29-year-old woman, also in Ha Tinh, is ongoing, the flood and storm control department said in its latest report.
Hundreds of homes, crops and portions of the national highway and railway -- linking north and south Vietnam -- have been submerged in flood waters.
In northern Cao Bang province, which borders China, a man was killed when a large tree fell onto his house in heavy rain.
Vietnam is frequently lashed by harsh weather in the rainy season between June and November.
Natural disasters including floods and landslides have left 136 people dead or missing in the country since the beginning of the year, according to the General Statistics Office.
More than 21,000 houses have been damaged, with more than 140,000 hectares of crops destroyed.
Scientists have warned extreme weather events globally are becoming more intense and frequent due to climate change.
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