Jacky Rowland, Al Jazeera's correspondent in Jerusalem, said: "People in Israel, by and large, believe that the army did a good job.
"There is no feeling among Israelis that heads should roll over the handling of the flotilla."
Barak said various alternatives were discussed in the weeks leading up to the raid and that he and other senior officials had considered the possibility that the activists would attack the troops when they landed.
"We regret any loss of life," the minister said. "But we would have lost more lives if we had behaved differently."
The minister's appearance before the five-member panel came a day after Benjamin Netanyahu, the Israeli prime minister, took the stand and insisted his country acted in line with international law when it stormed the boats in international waters.
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.
Gabi Ashkenazi, Israel's top general, will take the stand on Wednesday and was expected to be quizzed on operational aspects of the raid.
Threats to withdraw
Meanwhile, Israel has threatened it will pull out of a separate probe by the UN into the flotilla raid if the panel insists on grilling its soldiers.
The Israeli announcement came after the UN denied on Monday that it had struck a deal making Israeli soldiers off-limits for the probe.
The Israeli government has made clear that its soldiers would not be available to the UN investigators, who held their first meeting in New York on Tuesday.
Ban Ki-moon, the secretary general of the UN, was asked at a monthly news conference if the UN had agreed that Israeli military commanders could not be interviewed by the panel.
"There was no such agreement behind the scenes," he said.
"Their main work will be to review and examine the reports of the national investigations and liaise with the domestic authorities," said Ban.
"Whatever is needed beyond that, they will have to discuss among themselves in close co-ordination with the national government authorities."
After reacting coolly to the idea of a UN investigation, which is headed by Geoffrey Palmer, the former prime minister of New Zealand, Israel eventually agreed to co-operate with an investigative panel set up by Ban.
But Mark Regev, the Israeli government spokesman, said in Jerusalem on Monday that in the event Israeli soldiers are called by the panel to give evidence it could withdraw its cooperation.
In addition to reviewing the results of the Turkish and Israeli investigations, UN officials said Ban's panel will consider ways to avoid similar incidents in the future.