Two districts - Barpeta and Nalbari - have become the main concentration points of jihadi elements in the state, Gogoi said at a press conference here.
"Jihadi forces in Assam, who have links with the Jamaat-ul Mujahideen Bangladesh (JMB), are trying to raise a women's wing in Assam. Jihadi forces have already sent many youths from these two districts abroad for training," he said.
"We have already decided to hand over the cases of jihadi elements to the NIA. The jihadi issue has international ramifications and wider links. Our scope is limited to Assam only," he said.
Gogoi refused to comment on alleged links between madrassas and some political parties of Assam with jihadi activities, and said there was no proof.
"One or two people may be involved but that does not mean all are involved," he said.
Gogoi said there have been jihadi activities in Assam since 1995.
"We have made over 600 arrests, including elements from the Harkat-ul-Jihad-al-Islami (HuJI), and Muslim United Liberation Front of Assam (MULTA)," he said.
Meanwhile, seven people have been arrested in Barpeta district for their links with the Burdwan blast.
The National Investigation Agency (NIA), which is probing the Burdwan blast, has also launched an operation in Assam against Shahnur Alom, one of the main accused in the case who is now absconding.