Of the 46 seats the BJP bagged, ten were won uncontested before the polls.
The counting of votes, which started at 6 a.m., completed late Sunday afternoon.
The National People's Party (NPP) which won five seats in 2019 assembly elections, also won five seats – Liromoba, Longding-Pumao, Mariyang, Pasighat (East) and Tawang.
The Nationalist Congress Party (NCP) candidates secured three seats -- Bordumsa-Diyun, Lekang and Yachuli.
The People's Party of Arunachal (PPA) candidates won two seats -- Doimukh and Mebo.
Independent candidates -- Wanglam Sawin, Laisam Simai and Tenzin Nyima Glow -- have won the Khonsa (East), Nampong and Thrizino-Buragaon seats, respectively.
The Congress, which fielded candidates in 19 seats, has won the Bameng seat, where party candidate Kumar Waii defeated BJP candidate Doba Lamnio by a margin of 635 votes.
After the ruling BJP won 10 seats unopposed, elections for the remaining 50 Assembly seats were held on April 19, along with the Lok Sabha elections in two Parliamentary seats in the state -- Arunachal West and Arunachal East.
Chief Minister Pema Khandu was elected unopposed from the Mukto Assembly seat and Deputy Chief Minister Chowna Mein from the Chowkham (ST) seat.
Eight BJP nominees who have been elected uncontested are Dasanglu Pul (Hayuliang-ST), Dongru Siongju (Bomdila), Techi Ratu (Sagalee), Hage Appa (Ziro-Hapoli), Jikke Tako (Tali), Nyato Dukam (Taliha), Mutchu Mithi (Roing), and Techi Kaso (Itanagar).
Pema Khandu, the 45-year-old Monpa community leader, was elected to the state Assembly for the fourth time.
The BJP formed its first elected government in Arunachal Pradesh in 2019.
Khandu had formed the BJP government in 2016 after he, along with several MLAs, left the Congress for the People's Party of Arunachal and then joined the BJP.
The five-year tenure of the outgoing 60-member Arunachal Pradesh Assembly expires on June 2.
Around 78 per cent turnout was recorded in the Parliamentary polls and 83 per cent in the Assembly elections on April 19.
Altogether, 133 candidates were in the fray for the 50 Assembly seats and 14 candidates for two Parliamentary constituencies.
The counting of votes in the two Parliamentary seats would be taken up on June 4 along with the rest of the country.
The BJP had won both the Lok Sabha seats and 41 Assembly constituencies in the 2019 polls.
--IANS