Turkey has banned an Israeli military flight from its airspace in apparent retaliation for Israel's interception of the Free Gaza flotilla last month, in which nine pro-Palestinian Turkish activists were killed.

Officials in Ankara confirmed today that Israeli military aircraft would be permitted to enter Turkish airspace only on a "case by case" basis. There was no suggestion that civilian flights would be affected.

Israeli media reported that Turkey had not allowed a plane transporting military personnel to a tour of Holocaust memorial sites in Poland to cross its airspace. The aircraft, with more than 100 people on board, was forced to make a detour. Israel has not commented on the issue.

The move represents a further escalation of the crisis between the countries. Secular but Muslim Turkey, a Nato member, was Israel's most significant Middle Eastern ally, but the relationship has been battered by Israel's recent wars against Hezbollah and Hamas and by an eastward shift in Turkish foreign policy.

Tensions worsened last month over the Gaza incident, with Recep Tayyip Erdogan, Turkey's prime minister, demanding an apology from Israel. The foreign minister, Ahmet Davutoglu, compared the incident to the September 2001 terrorist attacks. Turkey is also insisting on an international inquiry, compensation for the nine victims — eight Turks and a dual US-Turkish citizen — and a lifting of the blockade of Gaza.

Israel has resisted calls for an international inquiry and has set up its own investigative commission, which includes two foreign observers. It held its first session today.

Turkey has recalled its ambassador to Israel and scrapped several joint military exercises. Israel's Ynet news website reported that other military flights had also been quietly cancelled. "Turkey is continuing to downgrade its relations with Israel," an unnamed official told Ynet. "This is a long-term process and not something that began just after the flotilla incident. We are very concerned."

Despite strained relations, a Turkish security delegation has visited Israel in the past month to examine remote-piloted vehicles purchased from Israel Aerospace Industries.