Pakke-Kessang recorded 86 per cent polling, while Likabali constituency recorded 51 per cent, Joint Chief Electoral officer D J Bhattacharjee said.
The polling percentage in both constituencies will increase as reports from several polling stations are yet to be received by the election office.
The polling, which began at 7 AM in the morning, was largely peaceful except for an incident of damage to EVM by a few unidentified men at Siberity, a booth in Likabali constituency where polling was suspended, Mr Bhattacharjee said.
"Technical snag developed in one EVM at Durpai polling station under Likabali due to which polling was suspended," he said adding re-polling would be ordered in both the booths.
Though polling was moderate during the morning hours due to chilly weather conditions, it gained momentum as the day progressed.
Elaborate security arrangements were made with state police, ITBP and four companies of central paramilitary forces being deployed. The critical polling booths were covered by CRPF and IRB personnel.
Altogether 150 polling personnel were deployed for Pakke-Kessang, while 220 polling personnel conducted the polling in Likabali, Mr Bhattacharjee said.
Former deputy chief minister Kameng Dolo of the Congress party is contesting against BJP nominee B R Waghe in Pakke-Kessang, while the Likabali constituency witnessed a multi-cornered contest by Kardo Nyigyor of the BJP, Modam Dini of the Congress, Gumke Riba of Peoples' Party of Arunachal and Independent candidate Sengo Taipodia.
The Likabali seat had fallen vacant after the death of state health and family welfare minister Jomde Kena in September.
The Pakke-Kessang fell vacant after the Gauhati High Court declared the election of Kameng Dolo from the seat in 2014 null and void, following an election petition filed against him by BJP nominee and former minister Atum Welly.
Mr Welly had alleged that a fraudulent move had kept him from contesting the election as the Election Commission had accepted a forged letter of withdrawal of his candidature that led to election of his lone opponent.
Mr Welly, in his election petition earlier, had said that his signature was forged in the letter.