The IMD has predicted isolated cases of heavy rain with lightning.
The Met Department has warned fishermen not to venture out to the sea along Kerala's coast on Tuesday.
The two districts wherein the alert was not sounded are Kollam and Thiruvananthapuram.
Only moderate rainfall expected in the state between December 3 and 9.
A low-pressure area is expected to form over the Andaman Sea by November 29.
Based on the IMD warning, Pathanamthitta, Alappuzha, Kottayam, Idukki and Ernakulam districts have been placed under yellow alert on Monday.
The Indian Air Force, NDRF, SDRF, Police and Fire Services personnel saved at least 64 persons, including a police inspector, from the massive flash floods.
Isolated rains are expected in various parts of Kerala for two more days.
Holiday has also been announced for schools in Nedumangad and Kattakada taluks in the Thiruvananthapuram district.
According to reports, a new low-pressure area is likely to form in the Andaman Sea in the Bay of Bengal in the next 12 hours.