A weekend of torrential rain caused rivers to overflow, flooding towns and villages and cutting off major roads, with many motorists left trapped in their vehicles for hours.
The number of evacuees across the country rose to about 51,000 on Monday, according to official data, with the worst-hit area being the eastern state of Pahang, where some 32,000 were forced from their homes.
The country's wealthiest and most populous state Selangor, surrounding the capital Kuala Lumpur, has been badly affected -- which is unusual as it typically avoids the worst of the monsoon floods.
Seven people have been confirmed dead in Selangor, according to fire and rescue officials cited in The Star newspaper. With reports of others missing, the toll is expected to climb.
Prime Minister Ismail Sabri Yaakob said that a month's rainfall came down in one day in Selangor, adding that tens of thousands of emergency service and military personnel were deployed to aid rescue efforts.
Student Eyilavarasi Magesuaran recalled the moment her house was flooded in the hard-hit city of Shah Alam in Selangor early Sunday.
"Water rushed into our house from the rear and back, trapping us inside," the 21-year-old told AFP, adding she was alerted to the flood by her barking dog.
"I really feared we would drown. We have lived here since 1995, and never experienced flooding."
A relative with a truck rescued her family.
The rains had largely stopped by Monday, leaving residents to return to damaged properties and pick up the pieces.
The Southeast Asian nation is hit by floods annually during the monsoon season, but those on the weekend were the worst in years.
Global warming has been linked to worsening floods. Because a warmer atmosphere holds more water, climate change increases the risk and intensity of flooding from extreme rainfall.