Gogoi reviewed the law and order situation in the state during a meeting and said the cases will be handed over to the NIA so that they can be probed thoroughly as they have "international ramifications".
"We have to take all possible measures to foil the sinister designs of anti-national elements. We will not compromise on national security and national integrity," he said.
At least six people were arrested in Barpeta district last month for their links with Bangladesh-based Islamist terror outfit Jamaat-ul-Mujahideen.
Police said at least two of them underwent training on jihadi activities in Bangladesh and were working with a sleeper cell of jihadi forces in Assam.
The meeting also decided to introduce the commissionerate system of policing in Guwahati.
"Guwahati would come under a police commissionerate with effect from Jan 1, 2015," he said.
"Due to rapid urbanisation, leading to burgeoning growth in the city's population, policing has become a greater challenge. The bringing of the fast-expanding city under a police commissionerate would infuse new vigour on the part of police to carry out the herculean tasks of combating crime, maintenance of law and order in society and generate a safe and secure environment," he said.