Twelve of 14 districts in Kerala are struggling with flooding after authorities were forced to open the gates to free excess water from 35 dangerously full reservoirs.
All rivers from northern district of Kasaragod to Thiruvananthapuram in the south are in spate.
Vijayan held emergency meetings with rescue officials in the state late on Wednesday and discussed the situation with Prime Minister Narendra Modi.
Vijayan said the heavy rains would continue for some more days, which will further worsen the situation.
Authorities have opened the gates of 34 reservoirs as water reached unsafe levels.
Cochin airport was shut till Saturday after water flooded the complex. Almost two lakh people have been living in relief camps while 14 teams of the National Disaster Response Force (NDRF), comprising 399 rescuers and 34 boats, were deployed in the state.
On Thursday morning, officials from Pathanamthitta have said that the water levels in certain areas have subsided but thousands are still stranded in their homes especially in the Ranni area where houses have been flooded up to the second floor, forcing the people to stay on the terraces.
The CIAL management on Wednesday said the airport would be closed until August 18 due to heavy rains and resultant flooding.
Indian carriers Air India Express, Jet Airways and IndiGo also operate services to Kochi from Doha.
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Kerala Chief Minister Pinarayi Vijayan's office announced on Twitter that Kochi's worldwide airport - the main gateway to the region - would be closed until Saturday "due to heavy rains and resultant flooding".
From the Cheruthoni dam, water is now being released at the rate of 8.5 lakh litres a second.
"Our state is in the midst of an unprecedented flood havoc", Vijayan said earlier this week. All airlines of Air India Express have been diverted to Thiruvananthapuram.
A landslide between Kuzhithurai and Eraniel stations has delayed four long distance trains, railway sources said adding a few passenger trains have been partially hit. Nearly all dams are opened.
Peermade in Idukki recorded the highest rainfall of 27 cm yesterday while Idukki town received 23 cm, Munnar 22 cm and Karipur in Malappuram 21 cm.
Currently, 239 camps are functioning in the district where 11,056 families have sought shelter.
The heaviest rains and floods since 1924 have caused massive destruction.
Bus services to Kochi were also affected after National Highways connecting the city submerged in Kalamassery area, officials said.