"There is now a heavy rain warning out for the northern parts of Johor and Pahang state as the rainfall there and the situation may worsen," deputy science minister Kong Cho Ha told Agence France-Presse.
"People's lives in these areas will be affected and so our advice to them is to monitor the weather warnings and act early when there is a warning," he said.
The state Bernama news agency said that in worst-hit Johor state in the south, 3,738 evacuees were sheltering at 42 flood relief centers and three major roads had closed.
In central Pahang state, 662 people have been evacuated to flood relief centers, two landslides were reported and two roads were under up to a meter (three feet) of water.
In northern Kelantan state, floods overwhelmed several villages and 185 people were evacuated, Bernama said.
Last December, large parts of Johor were flooded after days of heavy rain that left more than 110,000 people displaced.