The aircraft crashed in the river island around noon, soon after taking off from the Jorhat air base, they said.
The pilots killed in the crash were Wing Commander J James and Wing Commander D Vats.
"An Indian Air Force Microlight Virus SW-80 crashed around 1200 hrs today, after getting airborne from Air Force Station Jorhat, for a routine sortie," the defence ministry said in a statement in New Delhi.
A court of inquiry has been ordered to ascertain the cause of the accident, the ministry said.
The crash took place at Darbar Chapori, a sand bar in the Brahmaputra where there is no human habitation.
People from villages in the district spotted the aircraft going up in flames and informed the authorities.
IAF personnel from the 10 Wing Air Force Station in Jorhat rushed to the spot while police and senior officials of the district set out for the crash site, accessible only by boat.
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