Floods in Terengganu and Kelantan states forced authorities to shut down dozens of schools and roads to villages have been cut off.
The east coast regularly experiences tropical storms and heavy showers during the monsoon.
In the last two days in oil-rich Terengganu over a thousand people have been evacuated from their homes, and rescue officials predict the numbers will rise.
Che Adam Abdul Rahman, civil department force chief in Terengganu, told AFP that 700 rescue officers have been deployed in the state to carry out search and rescue operations.
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"We have now deployed boats and trucks to evacuate the villagers to relief centres, and with continuous rain we expect the number of flood evacuees to rise," Che Adam warned.
In neighbouring Kelantan, which experienced massive floods and large destruction of homes and public infrastructure in December 2014, at least 4,906 people have been displaced by flooding.
Zainuddin Hussin, Kelantan state civil department force chief, said some 1,300 personnel with 30 boats and 23 vehicles are involved in rescue activities.
"It is raining heavily and the water level at the Golok river has passed the danger level. Some schools in the state have been closed and many rural roads are closed to traffic," he said.
Schools in Malaysia were scheduled to reopen today after a month-long break.
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