Last weekend an Israeli commission charged with investigating the events surrounding the controversial Gaza aid flotilla of May 2010 made its report public.

Not surprisingly, the Turkel commission said (according to the Hebrew press) that the Israeli military acted in self-defense and did not violate international law when it boarded the Mavi Marmara aid ship. Israeli commandoes killed nine Turkish citizens on the ship, including one who held dual U.S.-Turkish citizenship.

A critical question is how the commission report will affect the prospects for Israel to repair the severe breach in Israeli-Turkish relations caused by the killings.

Turkey is a rising regional and global power and once was Israel’s closest Muslim ally. Israel needs a decent relationship with Turkey, even if Jerusalem can’t restore the warm ties the two countries once enjoyed.

On a trip to the region in October, during which I met with Turkish Prime Minister Recep Tayyip Erdogan, as well as with senior Turkish and Israeli officials, I felt there was still a chance for restoring normal relations. But that would require strong political will on both sides, including a readiness by Jerusalem to question the political thinking that led to the raid on the aid ship. Unfortunately, the Turkel panel has deferred the second half of its report, on the political aspects of the raid, for several months.

It’s still hard to fathom how the Israeli government made its decision. The Mavi Marmara was trying to run an Israeli blockade of Gaza and had been organized by a Turkish nongovernmental organization that Jerusalem believed to be hostile to Israel. But Israel had other options than boarding the ship at night in international waters in a fashion that was almost certain to encourage resistance. Had the ship been boarded in Israeli waters, or been disabled and towed to an Israeli port, the confrontation could have been avoided.

Moreover, Israelis still do not grasp the effect on Turkish public opinion of the deaths of nine Turkish civilians at the hands of a friendly country.

“We never had a case like this with any country in the region,” I was told by Ibrahim Kalin, foreign-affairs adviser to Erdogan. Another prominent Turk, who advocates Turkish-Israeli ties, told me unhappily: “Israelis don’t understand. No country can keep silent when nine citizens are killed on the high seas.”

Israelis also failed to understand that the emotional Erdogan took these killings as the latest in a series of personal affronts. The Turkish leader was hardly hostile to Israel. He had visited the country in 2005.

In December 2008, he invited Israel’s then-Prime Minister Ehud Olmert to his Istanbul home and spent hours relaying phone messages between Olmert and Syrian President Bashar al-Assad in an effort to restart direct talks between Israel and Syria. But Olmert did not tell Erdogan that Israel was planning to invade Gaza three days later. The Turkish leader felt betrayed, his mediation efforts ended, and ties between Turkey and Israel began to fall apart.

Erdogan’s subsequent emotional focus on Gaza convinced many Israelis he had become an enemy of their country. This was simplistic. Erdogan was genuinely upset by Israel’s refusal to permit many humanitarian goods into Gaza, including Turkish construction supplies that could have repaired the extensive damage caused by the Israeli invasion.

The assault on the Mavi Marmara further inflamed Erdogan’s emotions on Gaza; his rhetorical criticism of Israel grew shrill, and he withdrew Turkey’s ambassador from Tel Aviv. But he made clear that he would restore normal relations if Israel apologized for the killings and paid compensation to the families of the victims.

“As long as Israel does not apologize or pay an indemnity, we cannot easily re-establish our friendship with Israel,” Erdogan told me in his party’s headquarters in Istanbul in October.

“There are many similar incidents between friendly countries where one side has apologized,” I was told by Suat Kiniklioglu, spokesman for the Foreign Affairs Committee of the Turkish parliament. “If it doesn’t happen, it seems unlikely our relations will improve.”

Israeli emissaries met with top Turkish officials in Brussels, Belgium, in June and in Geneva in December, trying to find language that would satisfy both sides. They failed. Israeli Prime Minister Benjamin Netanyahu has said “there will be no apology,” although his country is willing to express “regrets” for loss of life. Israel’s hawkish foreign minister, Avigdor Lieberman, insists his country is “waiting for an apology from the Turkish government, and not the other way around.”

At this point, the only way out of the impasse seems to be the United Nations panel set up by Secretary-General Ban Ki-moon. Israelis and Turks told me the panel, led by former New Zealand Prime Minister Geoffrey Palmer, could help by coming up with some face-saving formula, but there is a catch: The panel only has powers to review the investigations conducted by Israel and Turkey and base its recommendations upon them.

Turkey finished its review long ago, but now the Turkel commission is delaying its final report. The longer the delay, the less likely the United Nations can be helpful, and the more likely crucial ties between Israel and Turkey will wither. Isn’t it time for Israel to consider whether it’s worth sacrificing some national pride in order to keep this strategic relationship alive?