"Military planes are required to obtain overflight permission before each flight. One military plane was denied permission immediately after," a Turkish diplomat was quoted as saying by the AFP news agency.
Another Turkish official said it was not a blanket ban and each flight request would be assessed case by case.
Yediot Ahronot, an Israeli newspaper, reported on Sunday that Turkey had barred a jet carrying Israeli military officers en route to a tour of memorial sites in Auschwitz, Poland, to fly over Turkish airspace.
The aircraft, carrying more than 100 officers, was forced to make a detour to reach its destination, the paper said.
The Israeli military "refrained from responding officially to the event so not to exacerbate the rift in relations", Yediot Ahronot said.
Ties between Turkey and Israel deteriorated dramatically following the flotilla raid, which saw Israeli troops boarding the lead ship Mavi Marmara, killing nine activists and injuring scores of others.
The action drew widespread international condemnation among the public as well as political leaders.
Israeli officials insist the troops involved in the raid acted in self-defence after allegedly being attacked by some of the activists on board.
Relations between Turkey and Israel had already soured after Israel's three-week war on Gaza in 2008-2009, in which around 1,400 Palestinians and 13 Israelis were killed.
Turkey has withdrawn its ambassador from Israel and cancelled joint military operations with the country in response to the convoy attack.
Ankara said it will not return its ambassador and will reduce military and trade ties unless Israel apologises for the raid.
The country also wants Israel to return the seized aid ships, agree to an international investigation and offer compensation for the victims.
"Up to now, we have done whatever is necessary within the rules of law, whether national or international and we will continue to do so,'' Anatolia quoted Erdogan as saying.
It said ties with Israel could return to normal if Israel meets Turkey's demands.
"We are not interested in making a show. We don't desire such a thing and
we have been very patient in the face of these developments,'' Erdogan is quoted as saying said.
Israel has objected to an international inquiry into its raid on the Freedom Flotilla and has set up its own investigative commission.
Jacob Turkel, the chief investigator of the Israeli commission, said on Monday it will summon Benjamin Netanyahu, the country's prime minister, to testify.
Ehud Barak, Israel's defence minister, and Gabby Ashkenazi, the military chief of staff, will also face the commission.
Under international pressure, Israel's government has included two foreign observers: David Trimble, a Nobel peace laureate from Northern Ireland and a member of the British House of Lords, and Brigadier-General Ken Watkin, Canada's former chief military prosecutor.