The Delhi Police had arrested Khoirom Ranjit Singh, the Commander-in-Chief of KCP and his woman associate Irungbam Sanatombi Devi from Mayur Vihar, and a third associate P Prem Kumar Meitei from Manipur in January, it said.
The case was later handed over to the NIA in March.
It had filed a charge sheet against the three arrested accused in July this year for allegedly being involved in terror activities.
Continuing its probe, the agency arrested Sanabam Inaobi Singh on November 29, an NIA statement said.