Patrick Cockburn: A blow to relations with its key ally in the Middle East

Israel's relations with its most powerful Muslim ally have plunged to a historic low, with the Turkish Prime Minister denouncing the killing of peace activists off the coast of Gaza as "state terrorism" and more than 10,000 protesters taking to the streets of Istanbul, with some trying to storm the Israeli consulate.

The Turkish government had not directly organised the flotilla of six ships – including the Turkish cruise ship Mavi Marmara – aiming to break the Israeli blockade of Gaza, but the foreign ministry had made clear before the Israeli assault that it supported the voyage as a humanitarian operation.

As Turkey recalled its ambassador yesterday, and cancelled three joint military exercises with Israel, Huseyin Celik, a spokesman for the ruling AK Party declared: "Our relations with Israel will never be the same."

The once-warm relationship has turned more sour and acrimonious over the past several years, but the attack on the Mavi Marmara, the fact that most of the dead are Turkish, and the pictures of Israeli commandos stalking past railings draped with the Turkish flag, will have an explosive impact.

The Turkish army used to favour links to Israel and the military used to control Turkish foreign policy. This is no longer the case. Prime Minister Recep Tayyip Erdogan and the Islamic AKP have weakened the military's grip on power since they formed a government in 2002. Willingness to co-operate with the US and support its alliance with Israel is no longer true of the younger officers as it is of the older generals. Yesterday's action against the Gaza aid flotilla was only the latest in a series of incidents between Israel and Turkey. In 2009, Mr Erdogan stormed out of a debate with Israeli President Shimon Peres in Davos when he was not given enough time to respond to Mr Peres's defence of the bombardment of Gaza.

Later that year, Turkey postponed an air force exercise because of Israeli participation; in retaliation, Israel sought stronger relations with Cyprus and Greece.

Other incidents followed. In an episode widely criticised as puerile in Israel, Deputy Foreign Minister Danny Ayalon summoned the Turkish ambassador this year to protest at a Turkish television programme which depicted Mossad agents snatching babies to convert them to Judaism. Mr Ayalon crowed that he had deliberately sat the ambassador in a lower chair than his own and removed the Turkish flag. Turkey later called for an apology.

Turkey is a more essential ally in the Middle East than it has been for years. It is playing a critical role in Iraq, helping the US to withdraw its forces more easily and Ankara's alliance with Israel has been a key plank of US diplomacy in the Middle East. The Turkish Foreign Ministry had warned earlier that Israeli action on the flotilla would have "irreversible consequences" and for once this diplomatic cliché may turn out to be true.