The National Disaster Management Agency said the weeks-long bout of bad weather was expected to carry on until tomorrow.
Dangerous water levels were detected in rivers in at least five states, a government monitoring website showed yesterday, with rising levels recorded in many other areas.
Some 50 people have been killed so far, a police Facebook post on Saturday said, with two still missing.
The tropical Southeast Asian nation often faces stormy weather around the year’s end, with seasonal flooding regularly causing mass evacuations.
But authorities have been taken by surprise by the days of constant rain that began on Dec 17, causing rivers to overflow and inundating cities.
Malaysia’s richest state of Selangor - the country’s commercial hub - has been among the worst-hit.
Around 117,700 of those evacuated since mid-December have returned to their homes, though nearly 10,000 people in five states on the country’s peninsular and in Sabah state on Borneo island have sought refuge in relief centres, official data showed.