Tokheho Yepthomi, fielded by the ruling People's Democratic Alliance (PDA), is leading over his lone rival of the opposition NPF by over 20,000 votes after the initial rounds of counting for the lone Lok Sabha seat.
Yepthomi belonging to the Nationalist Democratic Progressive Party (NDPP) secured 82,192 votes while C Apok Jamir of the Opposition Naga People's Front (NPF) secured 61,626 votes, EC sources said.
The PDA has the NDPP and the BJP as it major constituents.
The Congress has extended its support to the NPF candidate.
The bypoll was necessitated after Chief Minister Neiphiu Rio, who is also the NDPP leader, resigned as a Lok Sabha member in February, days before the assembly polls.