Vietnam's coastal provinces have been lashed by heavy rains since Sunday, with a record of up to 1.7 metres (five feet seven inches) falling over 24 hours.
Four people have been killed and another five are missing in Hue, Danang and Lam Dong provinces, the ministry said in a report.
More than 150 landslides had been reported, 2,200 hectares (5,400 acres) of crops destroyed and a total of 103,525 houses flooded, it said.
Many of the more than 21,000 people who were evacuated from the flood zone began to return home as water receded in the central coastal city of Hue on Wednesday morning.
However, more rain was reported by midday, forcing the local hydropower plant to discharge its reservoirs.
Central Danang province was also forecast to experience more flooding in the next two days, with Danang city's rivers swollen to alarming levels, the environment ministry said.
Scientists say human-driven climate change is making extreme weather events such as storms and floods more deadly and destructive.
Natural disasters, mostly storms, floods and landslides, left 187 people dead or missing in Vietnam in the first nine months of this year.
More than 240,000 hectares of crops were destroyed and 38,000 houses collapsed or were damaged, the General Statistics Office said.
Total economic losses were estimated at more than $610 million.
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