The FIR naming arrested suspected ISI agent Zakir Hussain was filed in the Special Court for bomb blast cases in suburban Poonamallee, the designated court for NIA cases in the state, police said.
NIA has taken over the probe from the Tamil Nadu Police.
A Sri Lankan national, 37-year old Hussain, arrested here on April 29, had told state police during interrogation that he was acting under instructions from his handler, allegedly an official in the Pakistani High Commission in Colombo.
He was part of a plot hatched from Sri Lanka to target foreign establishments in Chennai and Bangalore. The state Q Branch Police handling cases linked to national security was dealing with the case till its transfer to NIA.
The Tamil Nadu government consented to transfer the case to the national agency as probe had to be done in foreign countries including Malaysia, Sri Lanka and Maldives.
Two more persons, Mohammed Salim, 39 and Sivabalan, 45, a Sri Lankan national were also arrested on charges of supplying counterfeit Indian currency notes to Hussain. All the three are now lodged in Puzhal Central Prison here.
Hossaini was arrested for alleged conspiracy to carry out terror strikes on US and Israeli consulates in South India.
