"Overflight clearances are sought, and granted by other countries as per prescribed ICAO guidelines," said a source.
India will continue to seek such overflight clearances, sources said.
Citing alleged human rights violations in Jammu and Kashmir, Pakistan on Sunday denied India's request to allow Modi's aircraft to move in its airspace for his visit to Saudi Arabia.
In a statement on Sunday, Foreign Minister Shah Mahmood Qureshi said Pakistan has decided to not allow Prime Minister Modi to use the country's airspace, state-run Radio Pakistan reported.
He said the decision has been taken in context of the "black day" and in view of the alleged human rights violations in Jammu and Kashmir, it added.