The tense stand-off between Israel and its closest Muslim ally, Turkey, began to subside Thursday following Turkey’s acceptance of Israel’s second, stronger apology for its treatment of Ankara’s ambassador to Jerusalem. But the incident revealed a fundamental shift in the leadership and regional standing of the two countries that is likely to affect relations going forward.

Only a few weeks ago, Israeli Foreign Minister Avigdor Lieberman gathered together Israeli ambassadors from their postings around the world and announced a new style of Israeli diplomacy, says Alon Liel, former director-general of the foreign ministry. This new “national pride foreign policy” was, in his view, a direct precursor to Deputy Foreign Minister Danny Ayalon’s condescending behavior toward his Turkish counterpart this week.

“Already when we heard it, we were quite shocked. He said Israeli diplomacy is too soft and it has lost its pride. Many in the community of retired Israeli diplomats feel very ashamed at this, and in particular on what’s happened over the past week,” Dr. Liel says.

Earlier this week, Mr. Ayalon had called in Turkey’s ambassador to complain about a Turkish television drama that depicts Israeli intelligence agents and diplomats as murderous and cruel. As part of the official talking-to, Ayalon seated Amb. Oguz Celikkol in a visibly lower chair and did not place a Turkish flag as usual on the table along with the Israeli one – and made a point of noting this to the Israeli television crews filming the meeting. There were also no smiles or on-camera handshakes, though there were off-camera, leaving the Turkish ambassador feeling manipulated and insulted.

The 'end of the love affair'

Though the details of the spat may seem rather picayune, the backstory surrounding them foretells more potential changes in both Israel and Turkey.

Ayalon’s behavior, according to many Israeli political pundits, clearly came with sanction from Israel’s controversial foreign minister. Mr. Lieberman, the head of Israel Beytainu (Israel is Our Home) – a nationalist party whose election platform included a divisive plan to make Israeli Arabs sign a loyalty pledge to maintain their citizenship – began his tenure last year with a rocky start on the world stage. He had an early run-in with neighboring Egypt, and said he would recuse himself from any involvement in the Israeli-Palestinian peace process launched in Annapolis, Maryland, because he thought it was a waste of time.

But, Liel adds, the source of the latest crisis is not simply Lieberman’s or Ayalon’s approach to diplomacy on a world stage where Israel feels itself on the defensive, particularly in the aftermath of the Gaza war that raged at this time last year. Also changed is how Turkey’s leaders see their relationship with Israel.

“What happened between the two countries in the last 13 months, since December 2008 when the [Gaza] war began, signals the end of the love affair, and we have had a severe crisis going on that went all through 2009. We are deep inside it, it’s serious, and I am very worried that we don’t have change in 2010, we will see further deterioration,” Liel says.

Why warm ties are cooling

In general, Israel deeply values its relationship with Turkey, its closest Muslim ally. Turkey was the first Muslim country to recognize Israel in 1949. And an underlying sense of friendly relations goes back hundreds of years. When medieval Catholic Spain expelled its Jews in 1492 after the Inquisition, the Turkish sultan invited Jews to settle throughout the Ottoman Empire.

In recent decades, Turkey’s secular establishment – particularly its military – sought to upgrade the relationship with Israel for strategic purposes, seeing itself at odds with both Sunni Arab and Shiite Iranian fundamentalism.

But Turkey’s shifting domestic landscape has brought to power a government whose constituency does not support such close ties with the Jewish state. From the outbreak of the intifada in 2000 to the wars in Lebanon and Gaza, the past decade was marred with violent events that turned many average Turks against the alliance with Israel.

In addition, the politics of Turkish Prime Minister Recep Tayyip Erdogan, who came to power in 2002 as head of the Justice and Development Party (AKP), distinctly differ from his predecessors. The party, with strong roots in Islam, inherited the strategic alliance between Turkey and Israel – much of it based on cooperation by the countries’ militaries.

But the new Turkey, snubbed by the European Union and unsatisfied with the dividends of cooperating with the West, has warmed toward countries in the Muslim world that are at odds with Israel and the US. Tensions have run especially high over Israel’s military forays against Lebanon’s Hizbullah in 2006 and the Hamas-run Gaza Strip last year.

Both wars, which involved significant civilian casualties, have produced a public outcry in Turkey.

Erdogan has been one of the Middle East’s most vocal critics of Israel in both of these wars. At the same time, Erdogan sees himself as having taken a courageous risk, by working to reopen a channel for negotiations between Syria and Israel. Unofficial talks between Jerusalem and Damascus, achieved with Turkey’s help, broke off at the outbreak of the Gaza war last year.

“That track was an initiative of Erdogan,” and an apparent disappointment in Israel. “What we see now is that his government believes Israel is the side to be blamed for everything, for no progress in the peace process, both in the Israeli-Syrian track, as well as Palestinian,” Liel says.

Turkey looking east

One of the biggest changes in Israel’s perception of Turkey’s friendship has been that its seen as moving closer to having warm relations with Iran. This, says analyst Shlomo Brom, a retired brigadier-general from the Israeli army, is accompanied by the fact that Turkey’s military is no longer calling all the shots.

“Things have changed because there isn’t the same perception, as we once did, that we have common enemies. Turkey is no longer looking at Iran as their enemy, as they did then. The Turks are looking at themselves as a bridge between Middle East and the Western world in general, including Israel,” says Brom, an analyst of regional affairs at Tel Aviv University’s National Institute for Strategic Studies.

“The Turkish military is still interested in the relationship with Israel, but the power of the military is much less than it used to be. So what we’re seeing is adjustment pains,” he says. “I’m sure that our minister of defense [Ehud Barak] shares the view that the strategic relationship with Israel is of utmost importance, but I’m not sure the prime minister and other ministers do as well.”

Mr. Barak, who puts a premium on strengthening the relationship, is due to visit Turkey on Sunday – a point that caused some Israeli pundits to theorize that Lieberman was trying to sabotage Barak’s trip.

But the trip is still on, and the fact that Turkish officials said Thursday that they would push forward with a deal to receive Israeli drones in March - despite the diplomatic brouhaha – was a sign that the top military minds in both places still place high value on the relationship. Barak is to meet the Turkish defense and foreign minister, as well as the Turkish military’s chief of staff.