Overflowing rivers and a series of landslides have resulted in the death of 180 people as of Saturday morning, with over 3 lakh others forced to move to some 2,000 relief camps.
Modi, who arrived here from the state capital, is being accompanied by Kerala Chief Minister Pinarayi Vijayan, State Revenue Minister E. Chandrasekheran and other top state officials.
His visit comes at a time when the Congress-led opposition has been demanding immediate deployment of the Army since the state government has been unable to deal with the crisis.
Before returning to Delhi from Kochi later on Saturday, the Prime Minister will chair a meeting to discuss the situation.
Rains subsided on Saturday morning resulting in the water level in Idukki and parts of Ernakulam and Thrissur districts coming down.
But on Friday night, air lifting could not take place in Chengannur as the incessant rains continued in the region.