The court sent Sajil to judicial custody, NIA sources said, adding that they will seek his custody for interrogation.
Sajil had been absconding since 2010 after the attack on Thodupuzha New Man College professor T J Joseph for allegedly hurting religious sentiments through a question paper he had set.
The NIA court had in May last year sentenced ten people belonging to Popular Front of India, to eight years rigorous imprisonment for chopping off the hand of the professor.
NIA court judge P Sasidharan had also awarded two years rigorous imprisonment to three others in the sensational case and imposed a fine of Rs eight lakh on the 13 convicts.