By Agence France-Presse
But the number of people displaced in the states of Kelantan and Terengganu fell to about 18,300 from almost 23,000 Wednesday.
Seasonal flooding hits Malaysia's east coast states every year and regularly results in mass evacuations.
In badly hit Rantau Panjang, a Kelantan town bordering Thailand, more than 300 residents sought shelter at a crowded relief centre.
Evacuees said food was sufficient but there were hygiene concerns.
Dustbins were overflowing with garbage while families with young children were squeezed into small classrooms.
Looking glum, flood victims said they were worried about future supplies of clean drinking water, loss of income and thieves looting their homes.
Mohamad Nawi Che Mamat, 50, said he had to wade through floodwaters daily from the relief centre to check on his home.
"I am unable to go to work and have run out of cash," said the lorry driver, who supports a family of five.
Others who had chosen to remain in their flood-hit homes also expressed frustration, saying they have yet to receive aid.
"We are government supporters but we have not received any food aid from the federal government," said Abdul Manan Mohamad, who added he was running out of money to feed his wife and four children.
Mazlina Abdul Rahman, a 49-year-old single mother, told AFP she was hoping for food rations and cash assistance.
"I have to feed four children. I am running low on food supplies and do not have cash because my eldest child is unable to go to work due to the floods," she said.
From the air, parts of the state capital Kota Bharu resembled a muddy lake, with only rooftops peeking out of the murky brown waters.
In some areas in Kelantan, children were seen playing in floodwaters while commuters waded through knee-deep waters.
Zainuddin Hussin, chief of Kelantan's civil department force, said further scattered showers were expected.
Levels of major rivers were receding but he warned that the Golok river, on the border with Thailand, could overflow.
Malaysia's worst flooding in decades occurred in 2014 and forced some 118,000 people to flee their homes.
Prime Minister Najib Razak came under fire for golfing with US President Barack Obama during the crisis.
With a snap general election expected this year, Najib is expected to visit Terengganu and Kelantan on Saturday to oversee rescue efforts.
Votes from the two states will be crucial for the ruling United Malays National Organisation.