The aircraft crashed in the river island around noon, soon after taking off from the Jorhat air base, they said.
"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 pilots attempted an emergency landing but the aircraft crashed in a sand bar in the northern part of the district and went up in flames, Tezpur-based defence spokesperson Lt. Col. Harshvardhan Pande told PTI.
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.
The IAF had procured around 80 Slovenian-origin microlight aircraft about three years ago. They are usually deployed for environmental and bird recce missions, an IAF official said.