The president's office announced the order in a statement on Sunday after Israeli warplanes violated Lebanon’s airspace, flying over several parts of the country on Sunday morning.
"President Michel Sleiman tasked Foreign Minister Adnan Mansur with filing an urgent complaint to the United Nations about Israel's persistent airspace violations, including flying over all of Lebanon this morning, including the capital Beirut," a statement said.
AFP correspondents throughout the country reported unusually low and loud Israeli over-flights on Sunday morning, including in Beirut.
Israeli warplanes regularly violate Lebanese airspace and have launched several attacks against Syrian targets in recent months, some carried out from over Lebanon.
In May, the UN called on Israel to halt its increased violations over Lebanon as tensions soared after two Israeli aggressive airstrikes on Syria.
UN spokesman Martin Nesirky said then that the UN Interim Force in Lebanon, UNIFIL, had protested after recording a surge in Israeli flights over Lebanon.
He told a briefing, the over-flights are a "violation of Lebanese sovereignty and of Security Council resolution 1701" which allowed for a ceasefire that ended Israel's military incursion into southern Lebanon in 2006.