Netanyahu also accused Ankara of looking to gain from a high profile confrontation between Turkish activists aboard the flotilla's lead ship and the soldiers who seized the vessels in international waters on May 31.
"I am convinced that at the end of your investigation, it will become clear that the state of Israel and the IDF (Israeli Defence Forces) acted in accordance with international law," he told members of the Tirkel Commission.
Sitting in a chair facing the five-member panel and the two international observers, Netanyahu looked at ease as he explained that the naval blockade was crucial to efforts to prevent weapons from entering the coastal strip run by Hamas.
Netanyahu also said Israel exerted every diplomatic effort to have the ships in the flotilla turn back or dock elsewhere. But Turkey made no effort to halt the six-ship flotilla organised by the "radical Turkish organisation IHH (Foundation of Humanitarian Relief) which supports Hamas," he said.
"The Turkish government did not consider the confrontation between Turkish activists and Israel to be against its interests," the right-wing prime minister charged. Even so, Netanyahu insisted he had ordered troops to make "a supreme effort... to avoid harming anyone."
The PM evaded several questions, including whether Israel had considered alternatives to military action, saying he would respond during the closed-door session that followed the 90 minutes of public testimony.
Netanyahu was the first of three top officials to give sworn testimony about the assault on the fleet of boats trying to run the blockade on Gaza, killing nine Turkish activists and wounding scores of others.
The bloody raid caused a diplomatic crisis between Israel and Turkey and sparked global calls for an inquiry prompting Netanyahu's government to set up the Tirkel Commission to look into the legality of the operation.
Israel says its commandos resorted to force only after they were attacked when they rappelled onto the deck of the Mavi Marmara.
The soldiers "faced a very real danger to their lives from brutal attacks with clubs, metal rods and knives," Netanyahu said, adding the Turkish ferry "was no love boat and the IHH activists were not exactly innocent peace activists."
But activists have claimed troops opened fire as soon as they landed. The committee is only mandated to examine the international legality of the naval blockade and of the actions taken to enforce it.
Panel members are not authorised to probe the decision making process which led up to the operation, nor do they have the authority to question troops involved in storming the boats.
Hamas spokesman Fawzi Barhum said the commission could not be trusted because Israel was "trying to cover up its crime and is not telling the truth."
Defence Minister Ehud Barak will take the stand on Tuesday, a day before armed forces chief of staff Gabi Ashkenazi, with both likely to be quizzed over the operational aspects of boarding the ships.
UN chief Ban Ki-moon last week named his own panel to look into the deadly raid that is due to begin work on Tuesday and includes representatives from Israel and Turkey. On Monday, Ban denied having struck an agreement with Israel that would bar the UN team from grilling Israeli military personnel.
"There was no such agreement behind the scene," he told a press conference in New York. "The panel has a robust mandate, which is to examine and identify the facts and circumstances and the context of the incident as well as recommend ways to avoid future incidents," he said.
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