The neighbouring nation often sees stormy monsoon seasons at the end of the year, with seasonal flooding regularly causing mass evacuations.
Heavy downpours since Friday have caused rivers to overflow, submerging many urban areas and cutting off major roads, stranding thousands of motorists.
Almost 22,000 flood victims in eight states and territories were recorded on an official government website, with over 10,000 of them in the central state of Pahang.
More than 5,000 people fled their homes in the country’s richest state of Selangor - which surrounds the capital Kuala Lumpur - with Prime Minister Ismail Sabri Yaakob expressing surprise at the strong flooding there.
“In Selangor, the situation happened as if by surprise because the monsoon season... rarely has floods occurring in Selangor,” he said in a late-night press conference yesterday.
A government website showed water exceeding dangerous levels in six central and northeastern states this morning.
Dozens of bus routes in and around the Malaysian capital have been cancelled and train services leading to the port city of Klang were suspended.
While the rainy weather has slowed in some areas, the Meteorological Department warned that the downpour was expected to continue in parts of Pahang.
Malaysia’s worst flooding in decades came in 2014, forcing some 118,000 people to flee.