Nongdrenkhomba, who is the Chairman of Politburo Standing Committee and also the top most leader of the banned group, was yesterday arrested.
He was earlier arrested in Delhi, way back in November 2012.
One 9 mm pistol, 10 mobile handsets, 10 letterheads, foreign currencies, a PAN card, stamp seal of his outfit and other articles were seized from his possession, police said.
The 32-year-old militant has been remanded to police custody till April 11 by the Judicial Magistrate Imphal.
She was arrested by a team of 12th Bihar Regiment and Manipur police.
Based on her disclosure, another woman activist of the same group was also arrested by the police from the outskirts of the state capital. She has been identified as Laishram Manileima (45), the release said.