Qatar, which has faced a boycott by Arab states including the UAE since last June, said it had lodged a protest at the United Nations about the violation which allegedly took place on December 21.
The Qatari foreign ministry said on its Twitter account that it informed the UN secretary general and the president of the Security Council that the UAE jet "flew over the exclusive economic zone of Qatar" for one minute.
The ministry said "that the UAE plane entered the airspace of the State of Qatar without prior knowledge or approval of the competent Qatari authorities."
The UAE quickly denied the accusation.
"The Qatari complaint about the Emirati violation of its airspace is untrue and confused," UAE Minister of State for Foreign Affairs Anwar Gargash said on Twitter.
"We are working to respond officially to it with evidence and proof. What we see is an escalation and unjustified," he said.
"What has been happening under the table is now taking place in the open."
The four countries accuse Doha of supporting Islamist extremists and being too close to Shiite Iran, Saudi Arabia's arch-rival.
They have banned all flights to and from Doha and cut off most trade links.
Qatar denies the allegations, arguing the bloc aims to incite regime change in Doha.
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