The convict, KA Anoop, has been sentenced to six years in jail and a fine of Rs 1.6 has been imposed on him.
The case dates back to 2005, when a group of people hijacked and set ablaze a Tamil Nadu government bus.
The accused T Nazeer and others carried out the deed in support of their demand for the release of Abdul Nasar Madani, Chairman of Peoples Democratic Party (Kerala), who was detained in Coimbatore jail at that time.
After investigation, NIA charged 13 accused including KA Anoop under UAPA. Anoop, who was absconding abroad, was arrested in April 2016.
The trial of the remaining accused persons will continue, NIA said.