Southern state of Johor brought to near standstill as thousands flee homes.
Several others are reported as missing.
Relief coordination centres have been set up in the four states as well as Negeri Sembilan on the west coast with thousands of people seeking shelter in town and community halls as well as schools.
“Our focus is on how to get aid to the flood victims,” said Shafie Apdal, the minister in charge of domestic trade and consumer affairs.
Suriati Kamarul, who was forced from her home in Johor, said floodwaters rose to her shoulders before she was rescued.
“I prayed with about 10 neighbours and their children as we waited for help,” she told the New Straits Times newspaper. “Luckily police arrive in the nick of time in a boat.”
Malaysia suffers severe flooding each year caused by heavy rains during the monsoon season from November to February.
The country’s meteorological department has forecast more rains, which could push up food and palm oil prices in one of the world’s leading growers.
Johor is a major oil palm and rubber growing region, and a key source of vegetables and poultry.
Plantation officials say heavy rains have slowed down the harvesting and transportation of palm oil.
Last December major floods in Johor left more than 110,000 people displaced in the worst floods in nearly 40 years causing at least $451m in damage.