Flooding hits the country's east coast during the rainy season annually and often results in mass evacuations, but people in some areas said this year's are the worst in decades.
The worst-hit state is Pahang, where over 21,000 have been evacuated in recent days, according to the social welfare department.
Four deaths have so far been reported in the states of Pahang and Johor.
This year's floods come against the backdrop of a worsening coronavirus outbreak in Malaysia, with some fearful they could be exposed to COVID-19 in crowded relief centers.
The government insists it has taken steps to prevent the virus spreading, including ordering officials to screen evacuated villagers.