"Military planes are required to obtain overflight permission before each flight. One military plane was denied permission immediately after" the May 31 raid which left nine Turks dead, the diplomat, speaking on condition of anonymity, said, without elaborating.
The diplomat did not specify whether the incident signalled a total ban on Israeli military flights using Turkish airspace.
There were no restrictions on civilian flights, the diplomat added.
The Anatolia news agency Monday quoted Prime Minister Recep Tayyip Erdogan as saying that his country had closed its airspace to Israel after the raid on the aid flotilla.
Erdogan, who was speaking in Toronto after the G20 summit, gave no further details.
His remarks followed a report in the Israeli daily Yediot Aharonot that an Israeli military plane taking an army delegation to Poland was denied permission to use Turkish airspace.
The cargo plane, carrying more than 100 officers on their way to visit Auschwitz, had to follow an alternate route, the report said.
After the attack on the Gaza aid ship, Ankara had also recalled its ambassador to Israel immediately, scrapped plans for three joint military exercises and said economic and defence links would be reduced to a "minimum level".
Turkish officials have said Ankara will downgrade diplomatic ties with Israel if it does not take conciliatory steps, including an apology for the bloodshed and compensation for the victims' families.
Israel begins flotilla probe
Meanwhile, the Israeli commission investigating the legality of a deadly raid on a Gaza-bound aid fleet has officially begun its probe into the events of May 31.
The Tirkel Commission was set up two weeks after the Israeli raid in which nine Turkish activists were killed while scores of passengers were wounded.
The three-man committee is being led by retired supreme court judge Yaacov Tirkel. His work will be observed by two international observers.
The committe is expected to hear testimony from Israel's top political and military decision makers in the coming weeks.
The probe committee has been dismissed by Ankara, which has said Israel is incapable of being "impartial".
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