Natesan is the first accused in the case.
The others include Dr M N Soman, K K Maheshan, Najeeb and Dileep.
The development comes a day after a Vigilance court set July 27 deadline for the Vigilance and Anti-Corruption Bureau to conclusively state whether it had a case against Natesan and other office bearers of the Sree Narayana Dharma Paripalana (SNDP) Yogam.
Vigilance sources said an FIR was registered after a preliminary enquiry on the basis of several complaints, including that of CPM leader and former leader of opposition V S Achutanandan.
The case was filed on a complaint, among others, by Achuthanandan, accusing Natesan of siphoning off funds from microfinance ventures intended for the indigent in the Ezhava community.
Achuthanandan had contended that SNDP had availed Rs 15 crore loan from the Kerala State Backward Classes Development Corporation at an interest rate of two per cent and had charged 12 per cent interest from beneficiaries.
Meanwhile, reacting to the development, Kummanam Rajasekharan, state unit president of BJP, an ally of SNDP, said the registration of FIR against Natesan showed the LDF government's "intolerance".
In the last elections, Natesan had exposed the "anti- people" policies of UDF and LDF and it was in retaliation of the exposure that the FIR had now been registered, he alleged.
The SNDP was into microfinance for the past several years and no allegations had been raised so far, he pointed out.
The allegations were raised after Natesan floated a political party Bharat Dharma Jana Seva (BDJS), opposing both the fronts during the May 2016 assembly elections.
BDJS will not be nullified with these charges, he said, adding that the LDF government was protecting those who indulged in corruption worth crores of Rupees during UDF rule, and now hunting Vellapally by lodging a false case.
(REOPENS MDS9)
Meanwhile, reacting to the registration of an FIR against him, Natesan said he was prepared to face any enquiry.
"I am not scared of any investigation. I have not done anything wrong. The truth will come out," he told reporters at Alapuzha.
Natesan said he had no plans to "run away" or leave the country and has no plans to resign as SNDP chief.
KPCC president V M Sudheeran said Natesan should resign in the wake of the FIR against him over the alleged irregularities in the microfinance case.
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