AMMAN, Jordan Prime Minister Benjamin Netanyahu of Israel on Friday apologized in a personal phone call to Turkeys prime minister

r for a deadly commando raid on a Turkish ship in 2010, in a sudden reconciliation between the two countries that was partly brokered by President Obama during his visit to Israel this week, according to Israeli, Turkish and American officials.

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President Obama with President Shimon Peres, left, and Prime Minister Benjamin Netanyahu in Jerusalem on Friday.

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In the call, Mr. Netanyahu expressed regret for the raid, which took place as Israeli troops were enforcing a naval embargo on Gaza, and offered compensation, Turkish and Israeli officials said. The Turkish prime minister, Recep Tayyip Erdogan, accepted Israels gesture in the phone call.

Afterward, officials from both countries said that diplomatic relations had been fully restored and that ambassadors would be reinstated. In a statement, Mr. Obama welcomed the call, saying, The United States deeply values our relationships with both Turkey and Israel, and we attach great importance to the restoration of positive relations between them, in order to advance regional peace and security. At one point, Mr. Obama, just before leaving for Jordan, got on the phone with both leaders as they spoke, one senior American official said. Israel and Turkey had cultivated close ties over many years, but the acrimony over the raid, which resulted in nine deaths, created a stubborn hurdle. Recently, Mr. Erdogan drew harsh criticism for saying that Zionism was a crime against humanity. Discussing the phone call, a senior Turkish government official said, The Israeli prime minister, in a phone call that lasted 10 minutes, apologized to the Turkish nation for all operational mistakes, evident in an investigation, that led to human losses, and agreed to offer compensation. Addressing the Gaza embargo that led to the tensions, a statement from Mr. Netanyahus office noted that Israel had also already removed a number of restrictions on the movement of people and goods to all the Palestinian territories, including Gaza, and that the openness would continue as long as quiet prevailed. The two leaders agreed to continue to work to improve the humanitarian situation in the Palestinian territories. On Friday evening, Mr. Obama landed in Jordan, where he is likely to confront pressure to help that financially struggling country cope with a desperate tide of refugees fleeing the civil war in Syria. It was Mr. Obamas first visit to an Arab state since the Middle East erupted in unrest two years ago, toppling leaders in Egypt, Libya, Tunisia and Yemen, and plunging Syria, Jordans neighbor, into civil war. He held talks with King Abdullah of Jordan later on Friday. Diplomacy aside, Mr. Obama spent his last day in Israel and the West Bank making pilgrimages to symbols of the Holocaust, modern Zionism, the Middle East peace process and Christianity. In coming here, Mr. Obama traded symbolism for a still-unfolding crisis in Syria. About 3,000 refugees a day are fleeing into Jordan, swelling the ranks of Syrian refugees to 460,000, equivalent to 9 percent of the kingdoms population. That has put a heavy strain on the Jordanian economy, a strain that is only partly offset by aid from the United States. Jordan is seeking increased aid from European and Persian Gulf states, which have lagged behind the United States in their support. Given a potential pool of three million or four million refugees in southern Syria, Jordanian officials fear that the daily influx could swell to as much as 50,000.

Mr. Obamas speech in Jerusalem, in which he appealed to younger Israelis to prod their leaders to pursue peace with the Palestinians, was warmly received in Jordan, where the king has been a steadfast, if somewhat despairing, advocate for the two-state solution. As he wrapped up his visit to Israel on Friday, Mr. Obama avoided politics for more universal themes. After rekindling the eternal flame and laying a wreath at the Yad Vashem Holocaust memorial in the morning, a solemn Mr. Obama spoke of a collective obligation not just to bear witness but to act against racism and especially anti-Semitism. Our sons and daughters are not born to hate, they are taught to hate, Mr. Obama said. The state of Israel does not exist because of the Holocaust, but in the survival of a strong Jewish state of Israel the Holocaust will never happen again.