Gogoi and his associates were accused in two cases under the Unlawful Activities (Prevention) Act, 1967.
The Independent legislator and his two other associates were on June 22 cleared of charges in the first case.
NIA special judge Pranjal Das did not frame charges against Gogoi and his three associates Dhairjya Konwar, Manas Konwar and Bitu Sonowal in connection with the Chandmari case in which they were accused of having Maoist links.
The NIA was investigating two cases, which were initially registered at Chandmari and Chabua police stations, related to the alleged role of Gogoi and his associates in the violent protests.
Gogoi is likely to be released later in the day after the court sends the release order to the jail. His three associates are already out on bail.