The north-east monsoon which has been wreaking havoc in the southern state of Johor since Tuesday is now also affecting neighbouring Negeri Sembilan and Malacca, and central Pahang state.
"The latest figures that we have tabulated show that a total of 45,448 people have been evacuated so far in Johor," said state deputy welfare head, Roslan Baba.
In the tourist state of Malacca, officials said some 5,573 people had been evacuated from their homes, with 500 people displaced in Negeri Sembilan and 309 in Pahang.
"The situation is under control, our relief efforts are going on smoothly and there have been no shortage of space for the victims," Roslan said.
Rescue workers were trying to reach villages which had been cut off after flood waters submerged roads and brought down telephone and power lines, he said.
The floods had also triggered some mudslides, Roslan added, forcing roads to be closed to traffic while rail services to east coast states and to the south, including to Singapore are still suspended.
Newspaper pictures showed the town of Segamat in Johor completely inundated, with only rooftops protruding from the brown waters, and cars floating down streets.
A meteorological department official said that the north-east monsoon season, which affects the northeastern states of Terengganu and Kelantan and the eastern part of Pahang in November, usually tapers off by the end of December.
"Things should clear up in the south by this weekend," said the officer.
On Wednesday some parts of Johor recorded rainfall of up to 663mm (26.5 inches) with an average of 401mm throughout the state, slightly higher than Tuesday's 400mm. A daily reading above 200mm is deemed high.