The single-engine jet fighter aircraft manufactured by Dassault Aviation was on a test flight after an upgrade carried out by India's Hindustan Aeronautics Limited (HAL).
"Both occupants sustained fatal injuries... Investigation into the cause of accident is being ordered," the defence ministry said in a statement.
Local media reports said the pilots tried to eject but were caught in flames as the plane exploded at the HAL airport in the southern city of Bangalore. No one was hurt on the ground.
India had signed a $2.4 billion deal with France in 2011 to upgrade 51 Mirage 2000 fighters, which were purchased in the mid-1980s, with new electronic warfare systems and radar.
Last week, the Economic Times daily said the upgrade of the multi-role aircraft had been hit by production delays on part of HAL.
Crashes involving fighter planes are not uncommon in India which is in the midst of upgrading its Soviet-era military.
Most of the accidents involve the MiGs that India bought decades ago from the Soviet Union, earning it the unflattering "flying coffin" tag.
Last July, the pilot of an MiG-21 jet died after the fighter jet crashed in northern Himachal Pradesh state.
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