Facing a rout in other parts of the country, Congress retained power securing three-fourth majority in the Arunachal Pradesh Assembly snapping up 40 of the 60 seats and leading in two.
The Congress's 40 seats, included 11 won uncontested.
The BJP bagged six seats, three more than 2009 elections, while the PPA mustered 3 and a lone seat went to an independent, election office sources said.
Two sitting BJP legislators Dr Tangor Tapak (Pasighat West) and Tapen Siga (Daporijo) lost along with many other stalwarts.
Prominent Congress winners included former chief minister Jarbom Gamlin (Liromoba), Speaker Wanglin Lowangdong (Borduria-Bogapani), deputy speaker Jomde Kena (Likabali, PWD minister Kumar Waii (Bameng), industries minister Tapang Taloh (Panging), food and civil supply minister Kamlung Mosang (Miao) and minister of the Department of Tirap, Changlang and Longding (DoTCL), transport and cooperation minister Newlai Tingkhatra (Kanubari).
Chief Minister Nabam Tuki had won uncontested from Sagalee constituency along with power electrical, rural development and panchayati raj minister Tanga Byaling (Nacho) and tourism minister Pema Khandu (Mukto).
They were among the 11 to be elected unopposed.
Congress lost in Nampong, Bordumsa-Diyun Khonsa West, Khonsa East, Nari-Koyu, Bomdila, Meriyang-Geku constituencies, Raga and Ziro-Hapoli constituencies.
The result of Kanubari constituency would be countermanded and re-poll announced soon as the winner Tingkhatra died on May 7 at a Gurgaon hospital following cardiac arrest, the sources said.
The BJP, which won nine and three seats during 2004 and 2009 assembly polls, managed to secure six seats -- Mariyang-Geku, Nari-Koyu, Nampong, Bomdila, Raga and Ziro-Hapoli and was leading in four seats.
The regional Peoples' Party of Arunachal which had won four seats in 2009, managed to win three seats -- Bordumsa-Diyun, Khonsa East and Khonsa West -- and was leading in two seats.
PPA chief ministerial candidate Laeta Umbrey was defeated by new comer Muchu Mithi of the Congress in Roing constituency.
The NCP which bagged five seats in the last election failed to open its account this time.
Tsering Tashi, second son of former chief minister Dorjee Khandu won the Tawang constituency as an Independent.