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Israel’s state comptroller issued a report this week highly critical of the government’s handling of the Mavi Marmara flotilla incident in 2010.

The report, issued June 13 by Micha Lindenstrauss on the eve of leaving his position, said Prime Minister Benjamin Netanyahu’s decision-making process was flawed and the strategy did not follow the recommended protocol.

In addition, the 153-page report said, key agencies were kept in the dark about what was happening, and the possibility of extreme or fatal violence was ignored. There also was no proper documentation of discussions surrounding actions taken against the Gaza-bound flotilla nor the decisions that were made, it said.

The Mavi Marmara leaves Israel’s Haifa port on its way back to Turkey in August 2010. photo/ap-ariel schalit

“The prime minister’s decision-making process took place without orderly, coordinated and documented team work, even though the senior political, military and intelligence ranks were aware that the Turkish flotilla was different from other flotillas,” the report said.

On May 31, 2010, Israeli navy commandos boarded the Mavi Marmara, part of a six-vessel flotilla that claimed to be carrying humanitarian aid, after warning the ship not to sail into waters near the Gaza Strip in circumvention of Israel’s naval blockade of the coastal strip. Nine Turkish nationals, including an American-born man, were killed in clashes during the incident. At least seven Israeli soldiers reportedly were beaten, shot or otherwise hurt in the clash.

Lindenstrauss also criticized Defense Minister Ehud Barak for not looking into whether the army was prepared to deal with a violent response from the Marmara’s passengers.

The report further criticized Israel’s public response to the incident, saying the government was silent for too long while Palestinian supporters capitalized on the tragedy in the media.

Many Israelis maintain that naval commandos opened fire in self-defense after pro-Palestinian activists attacked them and believe that Israel has a right to keep ships from reaching the Gaza Strip, which is controlled by Hamas militants.

“Israel’s democratic process includes institutional mechanisms for independent oversight and we thank the state comptroller for his work,” Netanyahu spokesman Mark Regev said in a statement.

“We reiterate that the panel established by the U.N. secretary-general to investigate the flotilla incident clearly ruled that the maritime blockade to prevent weapons reaching the terrorists in Gaza is legitimate self-defense and that Israel’s decision to intercept the flotilla was indeed legal under international law. Ultimately, weapons that reach Hamas in Gaza end up being used against Israeli civilians.”

The incident has been the subject of several investigations, both inside and outside of Israel. While the new report does not represent the first official Israeli investigation to assail the conduct of the 2010 incident, it is the first to specifically criticize Netanyahu.

Israel’s government-appointed Turkel Comm-ission found in its investigation that the government and the military behaved appropriately, and that the blockade of Gaza was legal.

The U.N.’s Palmer Comm-ittee also found the blockade to be legal but said Israel used excessive force while boarding the vessel.

Turkey’s inquiry into the incident deemed the Gaza blockade and the Israeli boarding illegal. Ankara has called on Israel for an official apology and compensation, and to lift the Gaza blockade. The deaths of the Turkish citizens battered Israel’s already frayed relations with Turkey, once a strong ally in the Muslim world. The two countries broke off diplomatic relations and military agreements after the incident.

Israel imposed a land and sea blockade on Gaza in 2007 after Hamas militants seized control there, saying it was meant to keep weapons from reaching the Islamic radicals. Hamas is sworn to Israel’s destruction and has killed hundreds of Israelis in suicide bombings and other attacks.

The flotilla, which departed Turkey with the Mavi Marmara at its head, tried to break through the blockade despite Israeli warnings against sailing to Gaza. Video footage shows Israeli commandos boarding the ship and then being beaten by the activists before any shots were fired.

JTA and the Associated Press contributed to this report.