Officials said a team from NIA's Kochi unit arrested Abdul Jaleel (41) in the wee hours from a house in Narath area where his wife was staying. He will be produced before a special NIA court in Kochi on Thursday.
The case pertains to the conduct of a secret training camp in Narath area by Popular Front of India operatives.
The men were trained inside a building owned by Thanal Foundation Trust in use of swords and explosives for executing terror attacks.
Jaleel was the officiating chairman of the foundation. A non-bailable warrant issued by the court and a lookout circular were pending against him in the case, the officials said.
The agency has also picked up another person, identified as Shihab, along with Jaleel for questioning.
A special NIA court in Kerala had early this year convicted 21 men of PFI in the case.
The court had found them guilty under several charges, including criminal conspiracy, membership of unlawful assembly, possession of arms and explosive substances, inciting communal disharmony, assertions prejudicial to national integration besides organising a terrorist camp.