The chopper was found in a deep gorge in a heavily forested area in Yupia district after a massive search operation was launched.
The helicopter was evacuating people, stranded due to landslides triggered by rains at Sagalee in Papum Pare district.
The Advanced Light Helicopter lost contact soon after its take off from Sagalee at around 3.50 pm on Tuesday before the rescue.
Papum Pare district official J.Pertin said the helicopter had made five sorties since it arrived there at around 10.30 am on Tuesday.
"In the sixth sortie to Naharlagun, for unknown reason, the crew did not take the last batch of nine civilians and took off from Sagalee with just one policeman, who was deployed to help the two crew members and then went missing," Mr Pertin had told news agency IANS.
"Successfully evacuated 169 stranded people that include women, children from flood affected areas of Sagalee and Dambuk through IAF," Mr Khandu had tweeted.
Sagalee is just north of Itanagar, Dambuk in Lower Dibang Valley is about 350 km east of Itanagar.
With inputs from IANS
Follow NDTV for latest election news and live coverage of assembly elections 2019 in Maharashtra and Haryana.
Subscribe to our YouTube channel, like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.