According to official sources, External Affairs Minister S M Krishna was "directly" in touch with country's Ambassador to Nepal.
"I am deeply saddened to hear about the tragic air crash that occurred earlier this morning near Jomsong airport in Nepal. I would like to convey my deep condolences to the families of all those who have lost their lives in this accident. Our thoughts and prayers are with the families of all those who have lost their near and dear ones," the minister said in a message.
Carrying 21 people, the Dornier aircraft belonging to the Agni Air crashed when it hit a hilltop near Pokhara while returning to the Jomsom airport, killing 13 passengers.
Eight people on board, including the three crew members and four Indians, have been rescued alive from the crash site, said an official at the Rescue Coordination Committee of Tribhuvan International Airport.
The injured people were taken to a nearby hospital in Pokhara where conditions of the four Indians were critical.