Speaking to reporters at a news conference in Abu Dhabi on Tuesday, Helal Saad al-Qubaisi, an air force brigadier general, said UAE military aircraft would fly other routes over Saudi Arabia to steer clear of a potential interception by Qatari fighter jets.
"Abiding by the international laws is vital regarding these things. Interception is a dangerous matter," al-Qubaisi said.
"Our national carriers and other carriers will be committed to rules of the Civil Aviation Authority for the sake of the safety of all passengers, regardless of their nationalities," he added.
"We lodged a complaint with the International Civil Aviation Organization to investigate these unprecedented incidents. We are now examining the emergency procedures and other related matters."
On January 15, Qatar denied claims by the UAE that its fighter jets intercepted two Emirati passenger planes en route to Bahrain.
The allegations against Qatar came after Doha filed two complaints at the United Nations over alleged violations of its airspace by Emirati military aircraft, incidents that took place on December 21 and January 3.
The UAE, along with Saudi Arabia, Bahrain and Egypt, have severed diplomatic ties with Qatar in June 2017, accusing it of harbouring "terrorism".
The quartet closed their airspace to Qatar-owned flights, closed the Saudi-Qatari border and cut off most trade links.
Doha has rejected the allegations and accused the Saudi-led group of attempting to infringe on its sovereignty.