The country is experiencing its sixth episode of continuous heavy rain from the annual monsoon season that started in November, the Meteorological Department said, warning it could drag on until April.
In December, tens of thousands of people were also evacuated due to flooding.
The department warned that rain will persist in Johor and other parts of the country that could cause further flash floods Thursday.
The army evacuates residents in southern Johor state, Malaysia, on March 1, 2023. Rescuers in boats helped flood victims trapped on rooftops as heavy rain submerged homes in parts of Malaysia. (National Disaster Management Agency via AP)
Social media posts showed photos of a road that had collapsed due to overflowing water after a heavy downpour, vehicles and homes submerged in muddy waters, and shuttered shops.
In Johor, authorities said a man driving to work in a palm oil plantation was found dead after rescuers retrieved his car, which had been washed away by floodwaters.
Images posted by the National Flood Disaster Agency showed rescuers wading chest-deep in some areas in Johor to help victims trapped in their homes and carrying a baby in a bucket to safety.
The agency warned that waters in 25 rivers nationwide have reached dangerous levels. Data showed that 102 landslides have occurred since November due to heavy rain, it said.