The plane was travelling from the UAE to Bahrain on January 3 when it flew over Qatar's special economic zone "without prior authorisation", the foreign ministry said.
Yesterday Doha said it had lodged a protest at the United Nations about a UAE fighter jet violating its airspace on December 21.
In its new complaint, Qatar said the "repetition of this terrible incident" was evidence of the UAE violating international law.
UAE Minister of State for Foreign Affairs Anwar Gargash yesterday denied the accusation relating to the first incident and said Abu Dhabi would send an official response.
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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