The bodies were airlifted to Kathmandu on Monday, according to Agni Air staff.
The Indians were among 15 persons who were killed when a small plane with 21 people on board crashed in northern Nepal on Monday after hitting a hill top while attempting to land at a high-altitude airport.
Six others, including three Indians and two Danish nationals, miraculously survived the crash of the Dornier 9N AIG aircraft belonging to the private carrier Agni Air.
The bodies are now at Tribhuvan University Teaching Hospital in Kathmandu and the process of postmortem has been initiated, the airlines sources said.
Once the postmortem completes, the bodies will be handed over to the kin of the victims under the supervision of the Indian Embassy, they said.
The plane, which flew from the resort town of Pokhara on its way to Jomsom, crashed while landing at the mountain airstrip. The engine failure is said to be the cause behind the crash, according to the preliminary investigations.
Three Indians, including two children, who survived the accident are currently under treatment at Manipal Teaching Hospital in Pokhara and are out of danger, an official said.
They will be discharged after 4-5 days from the hospital, he said.