Results of 42 seats of the 60-member House have been declared so far.
The NFP, which has been in power in the state since 2003 except for a three-month-long break during the President's Rule in 2008, is ahead in four seats.
Chief Minister and NPF leader T R Zeliang won from Peren constituency by a margin of 5,432 votes.
The BJP won nine seats and is leading in two, whereas its alliance partner the Nationalist Democratic Progressive Party (NDPP) got 10 seats so far and is ahead in six constituencies.
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NDPP chief Neiphiu Rio, a former three-time chief minister, has already been declared elected uncontested from Northern Angami II seat.
The National People's Party (NPP) has won a seat and is leading in two. The party is an ally of the BJP at the Centre and in Manipur.
The Janata Dal (United), which shares power with the BJP in Bihar, is ahead in one seat.
An Independent candidate has also registered victory in the widely-contested state poll.
To form a government in Nagaland with a 60-member House, a party or coalition requires a minimum of 31 seats.
The election process in the north eastern state had started on a difficult note.
Following a no-poll diktat from the Core Committee of Nagaland Tribal Hohos and Civil Organisations advocating "solution (to the Naga political issue) before election", political parties initially kept away from the poll process.
Though filing of nominations started on January 31, the first batch of 22 contestants filed their papers only on February 5, the penultimate day for filing of nominations.
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