It said a total of eight aircrew and five passengers were onboard the aircraft and that the IAF is coordinating with Indian Army as well as various government and civil agencies to locate the missing aircraft.
The IAF has deployed C-130J and AN-32 aircraft besides two Mi-17 choppers while the Indian Army has pressed into service advance light helicopters to locate the missing Antonov AN-32 aircraft.
"The search operations from air and by ground parties of Indian Army are planned to continue through the night," the IAF said.
Defence Minister Rajnath Singh said he had spoken to the vice chief of the force on steps to find the missing aircraft and was praying for the safety of all those on board.
"Spoke to Vice Chief of @IAF_MCC, Air Marshal Rakesh Singh Bhadauria regarding the missing IAF AN-32 Aircraft which is overdue for some hours.
"He has apprised me of the steps taken by the IAF to find the missing aircraft. I pray for the safety of all passengers on board," the minister tweeted.
Chief of Air Staff Air Chief Marshal B S Dhanoa is in Sweden on a four-day visit which began Monday.
Official sources said the IAF has deployed all available resources to locate the aircraft.
The AN-32 is a Russian origin aircraft and the IAF currently operates a sizeable number of it.
It is a twin engine turboprop transport aircraft.
Officials said the Mechuka Advanced Landing Ground is around 35 kms away from the China border.
An AN-32 aircraft had crashed near a village in West Siang district of Arunachal Pradesh in June 2009 in which 13 defence personnel killed.
The aircraft had crashed over the Rinchi Hill above Heyo village, about 30 km from Mechuka advance landing ground.
In July 2016, an AN-32 aircraft went missing while taking off from Chennai for Port Blair with 29 people on board.
The aircraft could not be traced following weeks of massive search operations covering 2,17,800 square nautical miles by multiple aircraft. Months later, an IAF court of inquiry concluded that it was unlikely that the missing personnel on board the aircraft would have survived the accident.