Principal rival Congress on the other hand managed to get only eight seats, 15 less than in the last assembly election. The NCP won four seats and the BJP and JD(U) one each while Independents and smaller parties won eight.
Elections were held in 59 seats as polling was postponed in one seat following the death of a Congress candidate.
The BJP-led NDA had propped up the NPF during the 2003 assembly polls in Nagaland.
The association helped NPF lead the Democratic Alliance of Nagaland government for two successive terms. The 2013 verdict has given it a 'difficult' choice of forming its own government or sticking with NDA allies.
"Our voters have made it clear that they want us to pursue the issue of integrating the Naga people besides improving the standard of living," said CM Neiphiu Rio who won.
The NPF win has established Rio as the most charismatic leader after Jamir, who ironically was the former's mentor.