The accord was inked in the presence of Prime Minister Narendra Modi and Home Minister Rajnath Singh. National Security Adviser Ajit Doval was also present.
NSCN-IM leader T Muivah, who signed the pact, described it as a momentous occasion.
In his brief comments, he praised Mahatma Gandhi who, he said, had understood and respected the Nagas.
He lauded the "visionary leadership" of Prime Minister Narendra Modi.
Prime Minister Narendra Modi too commended the efforts of Home Minister Rajnath Singh and said this move will give way to a new future for Naga people.
"I join the nation in saluting you and conveying our good wishes to the Naga people," PM Modi said.
"Since becoming Prime Minister last year, peace, security & economic transformation of North East has been amongst my highest priorities," PM added.
"Unfortunately, the Naga problem has taken so long to resolve because we did not understand each other," added PM Modi.