"Some jehadi activities are going on. There is no doubt about that," Gogoi told reporters after a meeting with Home Minister Rajnath Singh here.
However, he said there was no evidence against All India United Democratic Front (AIUDF) being involved in it.
This comes after few men were arrested from the Assam's Barpeta district based on evidence linking them with Jamaat-ul Mujahideen Bangladesh (JMB).
Gogoi also said that his government was co-operating with the National Investigation Agency (NIA) on this issue.
"We are co-operating with the NIA from the very first day...it will be easier for the NIA to go to the origin," he said.
Gogoi also met Prime Minister Narendra Modi in New Delhi on Wednesday.