Rescue work was being hampered by heavy rain, local legislator TG Rinpoche said, adding the death toll could mount further with unconfirmed reports of a van with seven to eight people going down a gorge.
"So far about 12 people have died in separate incidents. Most victims died after hillocks caved in on their houses or they were washed away in flash floods caused by unseasonal heavy rains for the past four days," Rinpoche said.
The casualties occurred in and around the West Kameng district of Arunachal Pradesh, bordering China.
"More than 150 houses were damaged in the landslides, besides roads being washed away at several points cutting off surface links," Rinpoche said.
"We are unable to carry out rescue operations due to heavy rains. We don't know how long it would take to restore road links," a police official said.
Disruption in road links have led to restriction in movement of Indian Army soldiers to forward posts along the Chinese border.
"With road links snapped, we are facing problems although restoration work is on to clear the road soon," an army commander said.
On Tuesday, about 150 villages were inundated following flash floods in the adjoining Assam state. More than 10,000 people were displaced.
"Flash floods occurred in some districts of Assam after Arunachal Pradesh released excess water from a hydel power project. Floodwaters have since receded and all those who were displaced returned to their homes," an Assam government spokesman said.