While the waters were beginning to recede today, more bad weather was forecast over the next two days, with intermittent to heavy showers predicted for the northeastern states of Kelantan, Terengganu and Pahang.
The region is regularly hit by flooding during the annual monsoon, between November and March, but this year's storms have been unusually powerful.
"In my 42 years of living in Kelantan, I have never witnessed such a storm and destruction," said Ee Su Chuong, 42, the owner of an auto repair shop in Kota Bharu in Kelantan - the worst-hit state.
Ee also said that electricity had not been fully restored in Kota Bharu.
Also Read
As waters receded, images of overturned vehicles and victims returning to their homes to salvage their belongings were splashed across local newspapers.
Another area badly affected by the storm is Kuala Krai district, also in Kelantan - one of Malaysia's poorest states - where thousands of homes are totally submerged.
"I hope there isn't a third wave like people have been saying," Kuala Krai resident Maznah Abdul Rahman, 55, was quoted as saying by The Malay Mail.
Najib also ordered all his cabinet ministers to return to work, cutting short their traditional year-end holidays to manage the flooding crisis.
Truck drivers have complained of diesel shortages as many petrol stations have been submerged. At relief centres, workers are struggling to cope with a lack of clean water and unsanitary conditions.
The government has postponed the start of the school year by one week in light of the floods.