The ruling Naga People's Front (NPF) also secured 27 seats, running neck and neck with the BJP-NDPP combine.
According to EC sources, the BJP secured 11 seats while its alliance partner the Nationalist Democratic Progressive Party (NDPP) got 16 seats.
Expressing confidence about forming the government in the state with poll ally NDPP and some smaller parties, Union minister Kiren Rijiju said "We have 29 seats and need only two more. There are letters of support coming from smaller parties."
Chief Minister and NPF leader T R Zeliang won from Peren constituency by a margin of 5,432 votes. Recounting is on for Peren seat, the EC sources said.
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The BJP and the NDPP had contested 20 and 40 seats respectively.
NDPP chief Neiphiu Rio, a former three-time chief minister, was declared elected uncontested from the Northern Angami II seat.
The National People's Party (NPP), which is an ally of the BJP at the Centre and in Manipur, bagged two seats.
An Independent candidate also registered victory in the state polls.
To form the government in Nagaland which has a 60-member House, a party or coalition requires a minimum of 31 seats.
The Congress failed to win a single seat in the state.
The Congress, which has given three chief ministers to Nagaland since the state's inception in 1963, contested only in 18 seats, two less than the BJP.
Rijiju said that as the BJP had electoral understanding with the NDPP, it has to go with the party. "The BJP and the NDPP are sitting comfortably", he said.
The election process in Nagaland 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.