Further heavy rainfall has been forecast for most parts of the state on Saturday, and authorities said they planned to implement controlled releases of water from dams to manage flows and minimise damage.
Rains are expected to subside to "light to moderate" levels on Sunday, India's weather office said.
A witness in a relief helicopter in Chengannur, a town in southern Kerala, saw people stranded on roof tops and waving desperately for help.
"The town looked like an island dotted with houses and cars submerged in muddy flood waters and downed coconut trees," he said.
Two circling navy helicopters dropped food and water in metal baskets and flown out at least four people, including a three-year-old child.
Anil Vasudevan, the head of the Kerala health disaster response wing, said his department had geared up to meet victims' needs.
"We've deployed adequate doctors and staff and provided all essential medicines in the relief camps," he said.
His teams were also making arrangements to minimise the risk of people contracting waterborne diseases once they return home after the floodwaters subside.
The rains have also disrupted transport networks in Kerala, a major destination for domestic and foreign tourists.
Some crops have also been inundated. The state is a major producer of rubber, tea, coffee and spices such as black pepper and cardamom.
Prime Minister Narendra Modi said on Twitter he would travel to Kerala "to take stock of the unfortunate situation".