The Antonov An-32, took off from the Jorhat airbase in the Assam state for the Mechuka military landing strip, in Arunachal Pradesh state.
It was carrying eight crew members and five passengers, official sources told broadcaster NDTV.
“I spoke to vice chief of Indian Airforce (IAF) Air Marshal Rakesh Singh Bhadauria, regarding the missing aircraft which is overdue for some hours,’’ Defence Minister Rajnath Singh said on Twitter.
“He has apprised me of steps taken by the IAF to find the missing aircraft. I pray for the safety of all passengers on board,’’ Singh added.
The flight had been scheduled to land at Mechuka in an hour, but the aircraft lost contact with ground forces 30 minutes after take-off, the report said.
The IAF had launched search operations to track the plane.
The plane is likely to have gone missing over the eastern Himalayan range, where the terrain is mountainous with a thick forest.
The landing and take-off approaches to Mechuka are extremely difficult.
In 2016, an Indian air force An-32 disappeared while flying over the Bay of Bengal.
A search-and-rescue operation was launched, but the aircraft was never found.
All 29 people onboard were presumed dead.