"Today we will file our complaint to the International Civil Aviation Organization about the two serious incidents, along with the evidence that we've gathered, and ask for the intervention of the council to stop Qatar from repeating the act," Saif al-Suwaidi, head of the general civil aviation authority, told AFP.
The United Arab Emirates said on Monday that Qatari fighter jets had "intercepted" two passenger flights headed for Bahrain, drawing a swift denial from Gulf rival Qatar.
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Abu Dhabi is also looking at re-routing flights to Bahrain to avoid Qatari airspace, as a feud between Qatar and its Gulf neighbours escalates.
"We are now studying changing the route to another one which is very far from Qatar," Suwaidi said.
"However that will take some time as we have to reach an agreement with Bahrain".
Bahrain and the United Arab Emirates have no diplomatic ties with Qatar, which lies between the two Gulf allies and is banned from using their airspace.
In June, Saudi Arabia, the UAE, Bahrain and Egypt broke diplomatic relations and most trade links with Qatar, accusing it of ties to Islamist extremists and Saudi arch-rival Iran.
Qatar denies the allegations and and accuses the four states of aiming to incite regime change.
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