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The Federal Railroad Administration (FRA) is the lead agency for the NEC FUTURE program. The FRA has worked closely with a number of key partners, including the Federal Transit Administration (FTA), a cooperating agency on the Tier 1 Environmental Impact Statement (EIS). The FRA also regularly coordinates with other U.S. Department of Transportation modal agencies.

The FRA also coordinates closely with the NEC Commission, an organization established through federal legislation to promote mutual cooperation and planning for the NEC. The NEC Commission members include representatives from the U.S. Department of Transportation, the corridor states and District of Columbia, Amtrak, and non-voting representatives of the freight railroads who operate over the NEC. Connecting states and commuter operators on the NEC have also been invited as non-voting representatives.

The FRA has also coordinated with state and federal environmental resource and regulatory agencies since the inception of NEC FUTURE. In 2012, NEC FUTURE was selected for participation in a pilot project on environmental collaboration. The year-long pilot project was a unique partnership with the White House Council on Environmental Quality (CEQ) intended to promote early collaboration with federal and state environmental agencies for efficient environmental decision-making. The pilot project helped to identify best practices for environmental collaboration during a complex, multi-state planning process. It also provided a foundation for ongoing agency coordination, including a Statement of Principles to guide future communication with resource and regulatory agencies.