Public transport system collapsed in many parts of central Kerala.
The rain and floods have destroyed and damaged hundreds of houses in the past week and caused significant losses to crops in the state known for its spices and coffee.
The worldwide airport at Kochi, a major port city, has also suspended flight operations until tomorrow.
More than 60,000 people have now entered relief camps and the army and navy have stepped up rescue operations in the southern state, using a helicopter to airlift people, a Kerala disaster management official said.
Prime Minister Narendra Modi on Thursday morning spoke to Kerala Chief Minister Pinaryi Vijayan to discuss flood situation in the state.
"This sort of a situation has never been faced by the state".
Authorities have opened almost all of the dams in the state - a desperate gambit meant to ease the pressure the rainfall has exerted on their structures, but that has further flooded low-lying areas nearby and left residents stranded on the small pockets of dry land they can find. "We are doing all that is humanly possible and rescue efforts are going on", Vijayan told a press conference in Thiruvananthapuram, asking people not to panic but take all precautions to keep themselves safe.
TV channels broadcast a video shared by a Christian priest seeking food and water for about 1500 people stranded at a religious centre in Muringur. The worst flood in the state since 1924 has wrecked havoc across the coastal state, with damages estimated to be more than Rs 8,000 crore. The victims were identified as A Velankani and Vigneshwaran.
The met office has predicted heavy rainfall till Saturday. "We have also asked the State Level Bankers Committee to see that when the compensation amount is transferred, they should not levy any charges", said Vijayan. The state sounded a flood alert for nine districts. The minister also said that all the six major rivers of Tamil Nadu including Cauvery, Bhavani Sagar, Vaigai, Thamirabharani, Kothayar and Manimuthar are in spate due to continuous rains, he said.
Krishna Kumar, a relief official, said there will be no immediate respite for thousands of people in state-run relief camps with more rain and winds forecast until Saturday.
The northern parts of Telangana and Andhra Pradesh also battled heavy showers for the second straight day.
The death toll in the Kerala deluge is likely to go up as hundreds of people stranded in flooded areas, especially in and around Aluva and Pathanamthitta-Chengannur areas, were unable to get help in the last 24 hours. In Telangana, the Godavari river and its tributaries are in spate, disrupting normal life in Adilabad, Mancherial, Komuram Bheem, Karimnagar and Warangal districts.
Indian fire and rescue personnel evacuate local residents from their homes in Aluva, Kerala, on Thursday.
Seven teams with one Gemini boat each are deployed in Ernakulam district at various places.