State Revenue Minister E. Chandrashekeran said Malappuram, Kozhikode, Kannur, Wayanad, Kasargode and Idukki districts were the worst affected areas.
"Three NDRF (National Disaster Response Force) teams have been deployed in Malappuram, Wayanad and Idukki. We have requested 10 more teams," he said.
Meanwhile, the Indian Meteorological Department (IMD) has predicted heavy rains in the state till August 14. Red alerts have been issued in Idukki, Malappuram, Wayanad and Kozhikode districts.
In the morning, a 50-year-old woman died after a tree fell over her house at Attapady in the Palakkad district. A 24-year-old woman died after her house at Panamaram village in the Wayanad district got flooded.
Residents of the Wayanad district said such heavy rains had never been witnessed, even during last year's floods.
Over 700 people were evacuated in the Nilambur area of the Malappuram district. A.P. Sunil, a police officer, said some people had refused to leave their houses. "If they don't shift on their own, they will be forced to leave," he said.
Kozhikode District Collector Sambhasiva Rao said situation was under control. "If people cooperate, rescue becomes easy. But we are ready for any eventualities," said Rao.
Barring the state capital district and neighbouring Kollam, the remaining 12 districts have been affected by rains.
Fishermen have been asked not to venture out because winds were blowing at 40-50 km per hour.
University examinations in all the affected districts have been postponed.
( With inputs from IANS )