Other disease outbreaks including dengue fever following last month's floods - which killed nearly 500 people and forced more than a million from their homes -have left 28 dead.
Local media reported three leptospirosis deaths on Monday.
Popular tourist destination Kerala was the worst hit state, with the total number of dead in India this year 1,400 across 10 states.
However, the risk of getting this kind of fever especially during the floods.
Talking to reporters after a meeting to review the fever-situation, Health Minister K K Shylaja said the government was ready with a plan to check the spread of different types of fever including leptospirosis.
At least 66 people have died in the state since August 22 due to the bacterial infection that spreads through the urine of dogs, rodents, and farm animals.... It affects human when they come in direct contact with the urine of infected animals or with a urine-contaminated surroundings.
Barring Kasargode district, rains and floods had affected all the other 13 districts of the state. Health department has issued alert in these regions which include flood hit areas of the western regions of Changanassery, Kumarakom, Vechoor, Thalayolaparambu, Kallara, Maravanthuruth and Vaikom. However, there will be high alert for another three weeks to keep a check on the cases to take quick preventive measures, she said.
Over a fortnight after the massive floods ravaged the state, affecting almost 55 lakh people, about 13,000 people were still in various relief camps, State Disaster Control Room officials said.
Dr Reena K.J., the additional director of health services, said the toll and infection rate would have been much higher if majority of the people had not taken the preventive medicine.
Earlier, it was being reported that there was a shortage of doxycycline which was causing many to panic.
"Any such natural calamity is usually followed by a sudden spike in cases of such diseases".
If treatment is delayed, rat fever could affect the liver, kidney, lungs and heart, leading to death.