Nine people were killed in the raid and 41 others were wounded, including five commandos.
Barak praised the determination and operational methods of the Shayetet 13 (Flotilla 13) soldiers, who cabled down onto the deck of the largest vessel where pro-Palestinian activists resisted their boarding with knives.
"I have come in the name of the Israeli government to say 'Thank you'," the defense minister told the soldiers at their base in Atlit in an effort to raise their spirits.
"You operated under difficult conditions and carried out your mission to prevent the flotilla from reaching Gaza. I trust all of the commanders here to investigate the operation in order to draw the necessary lessons for the next time," he said.
Barak, who arrived at the base by helicopter, was accompanied by IDF Chief of Staff Lt.-Gen. Gabi Ashkenazi and Navy commander Vice Adm. Eli Marom. He spoke with the unit's commander, and later with its officers and soldiers.
"You carried out your mission properly," Barak told the soldiers.
Barak, Ashkenazi and Marom are also expected to question the soldiers on the operation, from the initial phase of intelligence gathering until the raid itself and the brutal clash with the Gaza aid flotilla participants.
The cabinet is expected to discuss the international community's demand for an impartial investigation. The discussion will be based on the soldiers' testimonies.