The secret files are related to the Offsets clause in the deal and were found on the roadside in a Delhi locality recently, IAF officials said, adding that the file has been recovered.
"The IAF has ordered a court of inquiry (CoI) into the loss of the secret file which went missing from the defence ministry. The
ministry will order a separate probe into the incident as the file had gone missing from there," Air Vice Marshal M Matheswaran, Assistant Chief of Air Staff (Operations) stated.
The incident comes at a time when the multi-billion dollar deal has entered the critical stage after the IAF carried out extensive flight evaluation trials of the six participating aircraft.
The IAF had submitted its report to the defence ministry, which has to take a final call on the deal.
He said the IAF had ordered the probe under a senior official to find out how the file had gone missing from the ministry as it belonged to the air force.
"The secret file has been recovered and it is in our custody," he added.
However, it was not clear as to how and who recovered the file.
Under the Offsets clause in the defence production procedure, a foreign vendor bagging any deal worth over Rs 300 crore has to invest back at least 30 percent of the contract's worth back in Indian defence sector.
Under the M-MRCA deal, the offsets were pegged at 50 percent of the worth of the deal.
American F-16 and F/A-18, French Rafale, Swedish Gripen, Russian MiG 35 and European Eurofighter are the six contenders
participating the deal for supplying the aircraft to the IAF.