The allegations, made by NGO Centre for Public Interest Litigation, include allotment of bilateral routes to private airlines at the expense of the national carrier.
Nationalist Congress Party leader Praful Patel was the Civil Aviation Minister when the aircraft were purchased and taken on lease.
The bench of Chief Justice Jagdish Singh Khehar, Justice N.V. Ramana and Justice D.Y. Chandrachud said it would be open to the petitioner organisation to move the court if it was not satisfied with the outcome of the CBI probe.
Disposing off the PIL, the court expressed hope that the investigating agency would adhere to the deadline of completing the probe by June 2017.
The counsel for the petitioner organisation CPIL had sought a court monitored probe. But Chief Justice Khehar said one could understand the plea if the same government was there.
"When the government is different, (the) party in power is different... We must have faith in our investigating agency," the Chief Justice said.