The ruling BJP in Arunachal Pradesh was leading in 33 assembly seats while the National People's Party (NPEP) was ahead in six constituencies, according to the Election Commission of India.
Counting of votes for 50 assembly seats in the northeastern state began at 6 am on Sunday.
The BJP had already won 10 seats unopposed in the 60-member assembly, elections for which were held simultaneously with the Lok Sabha polls in the first phase on April 19.
The Nationalist Congress Party (NCP) is leading in four seats, while the People's Party of Arunachal (PPA) is leading in three.
The Congress is ahead in one seat while in two constituencies independents are leading after the third round of counting.
Despite rain across the state, hundreds of supporters of various political parties were seen standing near the counting centres.
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