Authorities in the southern state, which is home to 33 million people, have placed local agencies on the highest alert level in what has turned out to be Kerala's worst monsoon in almost a century.
Kerala is battered by the monsoon every year but the rains have been particularly severe since August 8, flooding hundreds of villages and prompting the authorities to suspend flights in and out of the region.
More than 50,000 have sought shelter in relief camps.
"Twenty five deaths were confirmed earlier in the evening. The situation is bad in many parts of the state and the number [of deaths] will likely increase," said a senior official from the Kerala State Disaster Management Authority.
Unconfirmed local media reports mentioned a much higher toll and cited ongoing efforts to reach many flooded areas.
The official added that authorities had issued a "red-alert" warning in all 14 districts of the flood-ravaged state, with heavy downpours expected over the next 24 hours in many of the worst affected areas.
Kerala Chief Minister Pinarayi Vijayan's office announced on Twitter that Kochi International Airport - the main gateway to the region - would be closed until Saturday "due to heavy rains and resultant flooding".
Vijayan held emergency meetings with rescue officials in the state late on Wednesday and discussed the situation with Prime Minister Narendra Modi.
The chief minister has requested the deployment of additional personnel from the Indian army, navy and other emergency forces who are already working across the state, famed for its pristine palm-lined beaches and tea plantations.
"Our state is in the midst of an unprecedented flood havoc," Vijayan said earlier this week. "The calamity has caused immeasurable misery and devastation."
Authorities have opened the gates of 34 reservoirs as water reached dangerous levels.
Vijayan's office on Wednesday said that the authorities were also worried about rising water levels in the massive Mullaperiyar dam, and urged officials in the neighbouring state of Tamil Nadu to release water from the reservoir.
Hundreds of villages have been flooded, more than 10,000 kilometres of roads and thousands of homes have been destroyed or damaged across the state, officials said.
"We have asked all airlines, domestic and foreign, to reschedule their Cochin flights either from Trivandrum or from Calicut," Suresh Prabhu, India's civil aviation minister said on Twitter.
"For international flights, this will require special dispensation which has been granted considering the emergency DGCA (Directorate General of Civil Aviation) is coordinating," he added.
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