"In a place where citations should have been given, someone failed to prepare a standard operating procedure," said Ya'alon.
Ya'alon, who was the acting Prime Minister on the day of the operation, reiterated that the decision was correct, though there were rooms for improvement.
He was on the duty of the Prime Minister on the day of the incident as Benjamin Netanyahu was out of nation. Ya'alon praised the troops for their bravery.
"The fighting on the deck was heroic and took place under impossible conditions. There were some malfunctions during the planning and operational stages. I warned of this before the incident," he said.
Israeli Defence Forces (IDF) have ordered a formal inquiry into the flotilla raid. The panel is expected to submit the findings by Jul, 2010.