"We used to always prepare for the rainy season in November and December," Mohd Noor Saad, a 57-year-old resident in the town of Yong Peng, in Johor's Batu Pahat district told Reuters.
"Each household had a boat, but now with the unpredictable weather, it seems that we are not prepared and it's become chaotic."
Authorities have set up more than 200 relief shelters for people displaced by the floods, the national disaster management agency said.
Floods in Malaysia are common during the annual monsoon season between October and March, but the downpour this week left many Johor residents scrambling to find shelter.
Carrying belongings out of her house in thigh-high water, cafe worker Kabibah Siam, 54, said she was resigned to fending for herself during the floods.
"What can we do? We cannot complain about our fate because everyone is in the same boat here," she said.
While Johor was worst-hit, there was flooding in other states too that displaced hundreds of people.
The meteorological department warned of more rain in coming days, mostly in the southern states.