Whilst Saudi Arabia and Israel do not have diplomatic ties, many perceive this confirmation to signal a small but unprecedented step in thawing relations between Israel and some Arab states.
Netanyahu said that Saudi Arabia has not granted overfly permission to Israeli national carrier El Al, which operates four weekly flights to Mumbai.
Air India has not published when it would begin its flights to Tel Aviv, with media speculating they were due to start later in March.
India's national carrier Air India on Wednesday began selling direct five-hour flights between Delhi and Israel's Ben-Gurion global airport.
The letter to the ICAO adds that this situation, "clearly violates the basic principle of reciprocity and equality as recognized in the global civil aviation industry" and "violates the provision of the Convention on worldwide Civil Aviation".
But the historic animosity has given way to cautious, if often denied, cooperation based on a shared enmity towards Iran.
Flying over Saudi Arabia significantly shortens the route's flight time.
"I am requesting that the ICAO, which has the power to enforce the provisions of the Chicago Convention, take action ...to procure equal permission for El Al to fly above Saudi Arabia", Usishkin said.
- CNN's Oren Liebermann, Sugam Pokharel and Zahraa Alkhalisi contributed to this article.