The four daily flights to Tel Aviv are still running. The defense contract signed in December has not been scrapped. But since Israel’s war in Gaza, relations with Turkey, Israel’s closest Muslim ally, have become strained.

Israel’s Arab allies stood behind it in the war, but Turkey, a NATO member whose mediating efforts last year brought Israel into indirect talks with Syria, protested every step of the way in a month of angry remarks capped when Prime Minister Recep Tayyip Erdogan stalked off the stage during a debate in Davos, Switzerland, on Jan. 29.

In the week since, both sides have taken pains to mend fences, with officials in Israel and Turkey making conciliatory statements.

“Turkey and Israel attribute a special importance to their bilateral relations,” Turkey’s deputy prime minister, Cemil Cicek, said this week. “We want to protect our relations with this country.”

But both sides acknowledge that some damage has been done, and while the full implications for the relationship are still unknown, many political analysts say they sense a shift.

“It’s not a business-as-usual relationship anymore,” said Cengiz Candar, a columnist for Radikal, a Turkish daily. “It’s a very uneasy sort of cohabitation in this region now.”

Turkey is unique in the Middle East for its robust relations with Israel. It was the first Muslim country to recognize Israel as a state, and it has built up more than $3 billion in annual trade with Israel, far more than for any other Middle Eastern country.

Mr. Erdogan encouraged the relationship, visiting Israel in 2005 with a group of Turkish businessmen and becoming the first Turkish prime minister to visit the office of Turkey’s chief rabbi after a synagogue was bombed in 2003.

But when it comes to Hamas, which controls Gaza, they disagree. Israel views it as a terrorist group and focuses on its doctrinal commitment to destroy the Zionist state. Mr. Erdogan sees other aspects: Hamas began as a grass-roots Islamic movement, and like his own Justice and Development party, also Islamic-inspired, was democratically elected against overwhelming odds.

“They identified with some parts of the Hamas story,” said Femi Koru, a columnist for Today’s Zaman, a Turkish newspaper. “They were also outcasts who were not allowed to join national politics.”

Turkish officials argue that Mr. Erdogan’s stance against the war was simply healthy criticism — words of warning from a close friend who sincerely believed that Israel had gone too far.

“Turkey has lost its patience with the status quo in the Mideast,” said a senior Turkish official, who requested anonymity because he was not authorized to speak publicly on the matter. “Gaza is the bankruptcy of the military solution.”

The official added, “Israel is there to stay, and Palestinians are there to stay, and they need to be talking right now.”

Israel, for its part, feels that Mr. Erdogan is no longer a disinterested party in the peace process, and though the two countries will remain allies, the trust is no longer as strong.

“He has burned all the bridges with Jerusalem,” said one senior Israeli official, who spoke anonymously because of the delicacy of the issue. “He won’t be seen as an honest broker anymore.”

While Israel said it went to war to end rocket fire by Hamas, Mr. Erdogan said he saw the war through the prism of democracy.

“The world has not respected the will of the Palestinian people,” he said in an interview with Newsweek on Jan. 31. “On the one hand, we defend democracy and we try our best to keep democracy in the Middle East, but on the other we do not respect the outcome.”

He also rejects Hamas’s use of violence. “I’m not saying Hamas is a good organization and makes no mistakes,” he said.

Mr. Erdogan’s stance has won him praise in Arab societies, which opposed Israel’s military campaign and chafe at their leaders’ support of it.

“In one stroke, he became the moral patron saint of the Arab world,” said Mr. Candar, the columnist. But some Turkish columnists criticized Mr. Erdogan for what they said was an implicit hypocrisy — raising the issue of the Israeli killings of Palestinians while failing to mention his own country’s abuses in the mostly Kurdish southeast during years of war there.

“One would naturally ask Erdogan, who stands up against violence imposed on people in Gaza, what he thinks about Kurds being killed in his own country,” wrote Ahmet Altan in the liberal Turkish daily Taraf.

The fallout has affected Israeli tourism to Turkey, which is down in recent weeks, according to Avi Mendelbaum of Unital, a Tel Aviv travel agency. He said that his agency alone could fill a plane of 180 tourists going to Turkey a year ago, but that this year five agencies have joined to fill the same flight. The economic crisis is partly responsible, he said, but other destinations have not been hit as badly.

But Israelis make up less than 2 percent of Turkey’s tourism industry, and it would be far more serious if there were repercussions in the United States, where Jewish groups have helped Turkey block a resolution that condemns the genocide of a more than a million Ottoman Empire Armenians from being discussed in Congress.

Abraham H. Foxman, director of the Anti-Defamation League, said that Mr. Erdogan’s criticism was “like a shock to the system,” but added that the league had not changed its opposition to the genocide bill in Congress. “It’s not a question of punishment,” he said. “There’s too much at stake in the relationship.”

As for charges that anti-Semitism is flaring in Turkey, Mr. Foxman said it was no worse than in any other country.

Though Turkey’s role as a mediator in the Middle East might suffer, the broader relationship will not, analysts said. A $141 million contract for surveillance equipment signed on Dec. 25 has not been canceled, said the Israel company that signed it.