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The plane had been operating as a charter ambulance flight on a route from Gaya, India, to Tashkent, Uzbekistan, and onward to Zhukovsky International Airport in Moscow.
In the last six decades, MiG-21s have been involved in 400 crashes.
The deceased pilot was identified as Wing Commander Hanumanth Rao Sarathi, officials said, adding that a high-level probe has been ordered into the accident.
One more person onboard the Yeti Airlines that crashed in Pokhara on Sunday is still missing.
Yeti Airlines' 9N-ANC ATR-72 aircraft took off from Kathmandu's Tribhuvan International Airport at 10:33 am and crashed on the bank of the Seti River on Sunday.
The video shows aircraft taking a sharp turn towards the left and then crashing and turning into flames.
On Friday, the three Nepal natives were at Anicadu in Pathanamthitta to attend the funeral of evangelist Mathew Philip.
The five Indians were identified as Abhisekh Kushwaha, 25, Bishal Sharma, 22, Anil Kumar Rajbhar, 27, Sonu Jaiswal, 35, and Sanjaya Jaiswal, a Yeti Airlines official said.
Reports said five Indians were among the 15 foreign passengers on board. There were 72 people on the twin-engine ATR 72 aircraft operated by Yeti Airlines.
Karipur witnessed a deadly air crash in August 2020 claiming 21 lives.