An Israeli commission formed after the deaths of nine Turkish activists aboard a protest ship in 2010 finished its work Wednesday and submitted a series of recommendations meant to improve the way Israel deals with charges of war crimes.

The Turkel Commission’s new report looked at the way the country’s security forces and legal system investigate and prosecute alleged violations of international law. The commission concluded that Israel’s system was largely in line with Western standards, but suggested a list of changes aimed at making legal watchdogs more independent, transparent and fast.

The first part of the commission’s report, which focused solely on the bloodshed aboard the Mavi Marmara and concluded that neither Israel’s raid nor the naval blockade of Gaza violated international law, was released in January 2011. Wednesday’s report, the second and final installment, marked a broader attempt to revamp parts of the Israeli legal apparatus and did not further investigate the incident. Though Wednesday’s report was certain to draw less attention than the first, it may well turn out to be the more important of the two. 

The new report is partially intended to deflect future international war crimes charges and prosecution by making sure the domestic legal system is able and willing to prosecute offenses by itself. The threat of international legal action is more potent now that the Palestinians are a UN observer state, a status that could enable them to press charges against Israel at the International Criminal Court in the Hague.

The way Israel currently investigates and prosecutes alleged violations “meets, for the most part, the country’s obligations under international law,” according to the report. “At the same time, however, the commission concluded that in certain places the investigating apparatus could be improved and in certain places the accepted policy could be changed.”

The key recommendations in Wednesday’s report focused on increasing the independence of the military advocate general, the army’s top legal official, and creating new expert army teams to investigate incidents and decide whether criminal investigations are warranted. The current practice of basing such decisions on each unit’s own internal inquiries should be discontinued, the report says. The report recommends forming a special investigative unit for operational incidents that will — for the first time — include Arabic speakers able to question Palestinians.

The report also calls for new legislation that would establish the responsibility of high-ranking officers and civilian leaders for illegal actions they did not do enough to prevent.

The commission was formed after the deaths of nine Turkish citizens who resisted the takeover of the Gaza-bound protest ship Mavi Marmara by Israeli naval commandos on May 31, 2010 — an incident that drew a wave of international condemnation and helped wreck Israel’s ties with Turkey.

Footage taken from a security camera aboard the Mavi Marmara, showing the activists preparing to resist IDF soldiers about to board the ship. (Photo by IDF Spokesperson / FLASH90)

Footage taken from a security camera aboard the Mavi Marmara, showing the activists preparing to resist IDF soldiers about to board the ship. (Photo by IDF Spokesperson / FLASH90)

That incident came on the heels of the critical UN inquiry known as the Goldstone Report, which charged Israel with war crimes during its three-week Gaza operation in late 2008 and early 2009. Beset by growing legal woes abroad, including the possibility that Israeli leaders and officers could face arrest in Europe, the government ordered the commission not only to look at the Mavi Marmara takeover but to investigate the way the country deals with all such charges.

Commission members and observers included Jacob Turkel, a retired Supreme Court judge, and retired general Amos Horev, as well as international experts like Nobel Peace Prize laureate David Trimble and Brig. Gen. Ken Watkin, Canada’s former military prosecutor.

The military advocate general, the army’s top legal authority, should be chosen like the country’s attorney general — by the recommendation of an expert committee, and not by agreement between the chief of staff and defense minister, as is currently the case, the report said. Regulations should establish his rank and no promotion should be allowed during his term. Both changes are meant to diminish the possibility that army brass will be able to sway the advocate general’s decisions.

Sarit Michaeli, spokeswoman for the Israeli human rights group B’Tselem, praised the report, saying it showed the commission ‘understands the problems of the system’

A time limit must be imposed on investigations, the report said, to prevent cases from stretching over months or years. In the case of the killing of Palestinian protester Bassem Abu Rahmeh by a tear gas canister fired by a soldier in the West Bank in April 2009, for example, the military prosecution has yet to decide whether to press charges nearly four years later.

In a particularly dramatic clause, the commission also called for the elimination of the Shin Bet’s internal investigations unit — which has not once recommended a criminal investigation against any agent accused of wrongdoing, according to an official who worked on the report — and the transfer of its authorities to the police.

Implementing the recommendations “will contribute to improving the efficiency of the investigative systems in keeping with the accepted standards of the most advanced nations,” the report said.

Speaking Wednesday at a security conference in Tel Aviv, the army’s current military advocate general, Maj. Gen. Danny Efroni, said some of the report’s recommendations, like dealing more quickly with complaints and forming a new investigations unit, are already being implemented.

“There is no basis to the claims made toward Israel that it allegedly does not uphold international law in investigating war crimes,” Efroni said. “We had no doubt about that, but I’m glad we’ve received the stamp of approval from a state commission with international observers.”

The question of whether Israel adequately pursues legal action against members of its security forces has been a sore point both internationally and internally. This week, the Israeli human rights group Yesh Din released a report according to which of 103 criminal investigations opened against soldiers in the West Bank last year, none have resulted so far in indictments.

Sarit Michaeli, spokeswoman for the Israeli human rights group B’Tselem, praised the report, saying it showed the commission “understands the problems of the system.”

B’Tselem gave testimony to the commission and feels “exonerated” by the conclusions, she said.

“Many of the problems we’ve presented over the years, and have been rebuffed, were finally accepted here,” she said. “If adopted, the recommendations will certainly improve the system of investigations.”

Israeli law gives the Supreme Court authority over the military justice system, and Israel’s current system for dealing with alleged violations, even before the implementation of the new recommendations, puts it in the “top bracket” of Western countries, according to Robbie Sabel, an international law expert at Hebrew University and a former legal adviser to the Foreign Ministry. 

Any army faces an “inherent” problem in investigating an incident such as one in which a civilian is killed, Sabel said: The military’s primary goal is to learn what went wrong and avoid the same outcome in the future, so it needs soldiers to freely report what happened — which soldiers are unlikely to do if they know they face criminal prosecution in the kind of inquiry required by any legal system.

“If an army investigation is going to be used to incriminate somebody, they’ll cover their backside,” Sabel said.

“No one has managed to perfectly solve this problem,” he said.

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Times of Israel defense correspondent Mitch Ginsburg contributed to this article.