Recep Tayyip Erdogan told reporters in Toronto that Turkey imposed the ban after the May 31 raid on a Turkish ship that was part of a six-vessel international aid flotilla, according to the state-run Anatolia news agency. The prime minister, who is in Canada to attend a summit of the Group of 20 major industrial and developing nations, did not elaborate.
On Sunday, Israel's Yedioth Ahronoth newspaper reported that Turkey had not allowed a plane carrying Israeli military officers, en route to a tour of memorial sites in Auschwitz, Poland, to fly over Turkish airspace.
The transport plane, with more than 100 commissioned and noncommissioned officers on board, was forced to make a detour, the paper said.
The Israeli military "refrained from responding officially to the event so not to exacerbate the rift in relations," the newspaper added.
Turkish aviation officials were not immediately available for comment.
State elements told Ynet on Monday that the IAF's cooperation with the Turkish air force has suffered a major blow, as well as collaboration between the two's countries militaries.
A senior state official said that Israel is concerned with the changes Turkey is undergoing. "This is not just the specific act of closing the airspace, but Turkey's process of abandoning the West and reaching out to the East."
The Prime Minister's Office refused to comment on the statements attributed to Erdogan on the matter. Nevertheless, a state official speaking off the record said, "Turkey is indeed pursuing a deterioration of its relations with Israel according to Erdogan's policy. Approvals for several military flights over Turkey have been withdrawn. It's a long process that didn't begin today or after the raid, but much earlier."
The source noted the harsh exchange of words between President Shimon Peres and Erdogan in Davos in January 2009 as an example. "We are concerned," he concluded.
Eight Turks and a Turkish-American were killed in the raid that drew Turkish outrage and widespread international condemnation.
The aid ships were sailing to Gaza to break an Israeli blockade imposed to keep weapons and other military components out of the hands of Gaza terrorists who have attacked Israel with bombs, rockets and mortars for years.
'We have been very patient'
Israel insists troops involved in the deadly raid acted in self defense after being attacked by some of the activists on board.
Turkey, which had a close alliance with Israel until the three-week Gaza war, which ended in early 2009, withdrew its ambassador and canceled joint military drills in response to the raid. It has said it will not return its ambassador and will reduce military and trade ties unless Israel apologizes for the raid. It 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, adding that ties with Israel could return to normal if the Jewish state 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," he said, according to Anatolia.
Israel has objected to an international inquiry into the operation and has set up its own investigative commission that includes two foreign observers.
The Israeli Transport Ministry told Ynet that the Civil Aviation Authority has not received any official notification from Turkey that it had closed its airspace to Israeli flights.
The ministry said Israeli passenger planes are continuing to fly through Turkey as usual.
Roni Sofer contributed to this report