During a meeting with NEC Secretary K Moses Chalai on Friday, Khandu rued that the NEC has become just a funding agency of late, as per an official statement.
"We have been having deliberations after deliberations but nothing concrete is coming out from NEC. I believe it has bigger roles to play," he said.
The NEC must reinvent itself as a regional think tank with a greater focus on key areas, he added.
Khandu said the NEC can be to Northeast what the NITI Ayog is to the country -- a one-point solution centre.
"Under Prime Minister Narendra Modi, we have the political will to transform the North East. It''s up to you (NEC) to come out with a roadmap," he told Chalai.
Stressing that an empowered NEC must provide mentorship for planning and oversight in all priority sectors, Khandu urged the agency to play the role of an institutional anchor for the Northeast states, and help draw a blueprint of comprehensive development.
He said funding should not be the sole agenda of NEC.
"We are lucky to have a secretary who hails from the region. You must take a personal interest and empower NEC as an agency to reckon with for the development of the North East," Khandu told the official who called on him.
He urged the secretary to suggest the way forward to all chief ministers of the region, who can then collectively work on it and impress upon the central government.
Explaining the diversity in demography and geography of Arunachal Pradesh, Khandu reminded Chalai of the complete dependence of the state on central grants and aids.
Due to complete denial of any international funding, Khandu said central government agencies, including NEC, need to give special preference to Arunachal Pradesh.
The chief minister suggested that the NEC authorities come out with a concrete plan on the new role of the agency that can be announced during the Golden Jubilee Plenary Session next year.
"Leading up to the NEC turning 50 in 2022, this is an opportune occasion to take a fresh look at its mandate and dwell upon a course of reform," he added.