The charge sheet named Laishram Ranjit Singh Meitei alias Tamnganba, commander in chief of KCP (People's War Group), Khumanthem Naobicha Singh and Thoudam Chaothoi Singh.
The agency claimed the accused raised funds through local persons and bodies such as schools, panchayats, government officials and owners of petrol pumps.
The charge sheet was filed under Sections 17 (raising funds for terror acts), 18 (conspiracy) and 20 (being a member of terror organisation) under the Unlawful Activities (Prevention) Act.
The accused were arrested by the Delhi Police's Special Cell last year. In October, the case was transferred to the National Investigation Agency (NIA).