The girls aged 6 and 9 were among three Indian survivors of the crash in which the Dronier aircraft got buried after hitting a mountain peak straddling the airport.
"The girls are conscious and out of danger," Indian Embassy spokesperson Apoorva Srivastav told news channels.
The third survivor, she said, was a 45-year-old man. It was not clear whether the parents of the young girls survived.
The girls and the man were part of a group of Indian pilgrims apparently from the South who were overtaken by ill fate on their way to a pilgrimage to the holy shrine of Muktinath.
"We are in touch with few of the relatives of the families," she said, adding that the control room number has been circulated and people have been contacting us.
Sixteen people, most of them Indians, died in the crash. Srivastav assured that rescue operations were in full swing as Nepal army personnel have rushed to the crash site.
"Nepal army personnel have left for the accident site to bring the remains of the deceased to Kathmandu. They are expected to reach Kathmandu by 4 pm," she said.
The aircraft which hit the top of a hill while landing at the Jomsom airport broke into pieces reportedly but did not catch fire.
The plane is now buried in the side of the hill. Rescue operations are underway as bodies are being airlifted from the site.
"All fifteen bodies have been recovered from the site and they are being airlifted to Kathmandu," a journalist said.