Jerusalem (CNN) -- The head of Israel's military defended the "bravery, morality and calm" of his commandos Wednesday on the third day of the nation's inquiry into Israel's mid-sea interception of a humanitarian aid flotilla that left nine people dead.
But Gabi Ashkenazi, chief of staff for Israel Defense Forces, acknowledged that "there was a lacking evaluation regarding the intensity" of the activists' "resistance and their intentions."
"We should have known more," he said at the inquiry. Nevertheless, he said, the "first shooting was by the activists on the boat and not by the IDF soldiers. This is a clear and founded fact."
The flotilla's organizers say the ships were headed to the Palestinian territory of Gaza with humanitarian aid on May 31. That's when Israel stopped the vessels as part of its naval blockade to thwart weapons smuggling to Gaza militants intent on attacking the Jewish state.
Naval commandos who boarded one of the ships, a Turkish-flagged vessel called the Mavi Marmara, fought with activists. The confrontation left one Turkish-American and eight Turkish activists dead, and sparking an international outcry.
Ashkenazi said stopping the flotilla was right and such an action "was to be made with minimum friction."
The navy commandos found themselves in a life-threatening situation and only shot the people they needed to shoot, said Ashkenazi, who noted that activists used weapons taken from soldiers.
"The activity of the commandos was praiseworthy, exercising remarkable restraint against those who called themselves peace activists," he said. "The force acted professionally while keeping purity of the arms and proportionally in light of the risk (they were facing)."
"The moment the activists decided to use cold and live weapons against the IDF soldiers, the conflict was inevitable. Even if we would have known of their intentions, the conflict there would still be a violent confrontation. The only difference there would be was inflicting less danger on the IDF soldiers," he said.
Ashkenazi explained that the "main gap" was the incorrect evaluation "of the intensity of resistance."
"Even in retrospect, I'm not sure we could have known," he said.
The commission investigating the raid questioned Ashkenazi about Turkish activists' claims of executions. He acknowledged that some were shot at close range, but said soldiers were under threat.
During his testimony, Ashkenazi gave a 15-minute video presentation, showing what he said happened during each step of the raid.
Echoing the sentiments of Defense Minister Ehud Barak, who testified a day earlier, Ashkenazi said, "As commander of the army, I carry responsibility for its actions.
Barak said Tuesday that he bears full responsibility for the actions of Israeli soldiers in the May incident.
He defended the action and said Israel went to great diplomatic lengths to stop the flotilla heading to the Palestinian territory of Gaza. When that didn't work, he said, they considered the implications of the use of force and weighed the possibility of simply letting the flotilla through.
In the end, Israel made the right decision, Barak said in his two-hour testimony.
"We regret any loss of life, but without the courage and skill of the commandos, we would have lost more lives," Barak said.
The incident affected the military and diplomatic alliance between the Jewish state and Turkey, its powerful regional ally.
U.N. Secretary-General Ban Ki-moon expressed hope that a separate U.N. inquiry, launched Tuesday, would help mend the strained relations. Ban met with members of the U.N. panel, which is chaired by New Zealand Prime Minister Geoffrey Palmer and includes representatives from Israel and Turkey.
But Israel has already said that it will not participate in the U.N. inquiry if the panel asks to question soldiers.
"Prime Minister Benjamin Netanyahu clarifies that Israel will not cooperate and will not participate in any panel that will demand to interrogate IDF soldiers," said government spokesman Nir Hefetz.
Netanyahu said Israel operated within international law when it stopped the flotilla and raided the Mavi Marmara on May 31.
"I'm convinced that at the end of your investigation, it will be clear that the state of Israel ... operated in accordance with international law and that ... soldiers on the Marmara showed great courage in fulfilling their mission and acting in self-defense against real-life dangers," Netanyahu said Monday, the opening day of the Israeli probe.
Israel has maintained its troops used force on the activists only after they were attacked by those onboard. Soldiers were attacked with knives, metal poles and other objects, Israeli officials have said. But passengers on board the boat insist they were fired upon without provocation.
The Palestinian territory has been blockaded by Israel since its takeover by the Islamic movement Hamas in 2007.
CNN's Paula Hancocks, Guy Azriel and Ed Payne contributed to this report.