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The military later said the soldiers were not expecting trouble and had paintball guns as their primary weapons while handguns were only for an emergency. Two activists grabbed the handguns away from soldiers and shot two of them, the military said at the time. Both activists were then shot and killed.

The fighting left nine activists dead, most of them Turks, and dozens were wounded. On the Israeli side, a total of seven soldiers were wounded.

Israel insisted that its soldiers acted in self-defense and later showcased knives, slingshots and clubs they said were found onboard the ship. Some activists had military-style gear, including bullet-proof vests and night-vision goggles. Israel said this indicated that the activists had planned for violence.

I am hopeful that today’s exchange between the two leaders will enable them to engage in deeper cooperation on this and a range of other challenges and opportunities

The activists also said they acted in self-defense and insist they were attacked first.

Israeli officials said Obama helped play a role in the reconciliation, but that efforts had been going on behind the scenes for some time.

Israel and Turkey were once close allies. But in recent years, ties have deteriorated with the rise of Erdogan’s Islamist party. Following the flotilla incident, Turkey withdrew its ambassador to Israel and greatly scaled back military and economic ties. But relations were never broken completely.

A statement from Erdogan’s office said Netanyahu had apologized on behalf of Israel for all kinds of mistakes that resulted in the loss of life or injuries in light of an investigation led by the Israeli side that pointed at a series of operational mistakes. “Our prime minister accepted the apology in the name of the Turkish people,” it said.