During a pre-taped interview airing Sunday, Ayalon told the weekly public affairs show Fareed Zakaria GPS that the sail's organizers were the ones who should apologize, but also stressed that Israel is trying to be responsible and restrained. He noted that relations with Turkey are important for both Israel and the United States.
According to the deputy FM, there were dozens of terrorists mixed in with peace activists on the flotilla.
"They were associated with al-Qaeda and other terror organizations," CNN quoted Ayalon as saying.
"They are graduates of Afghanistan or - or Iraq. They had a hierarchy," he added. "They were arranged in a military-type or paramilitary organizations. They were well equipped. And they were ambushing our soldiers. They occupied the higher deck - the top deck - to wait for soldiers.
"Unfortunately, on the Turkish ship, we saw two types. That out of 675 people on the ship, about 600 were peace activists, I would say naive peace activists, about 75 were mercenaries," Ayalon said. "We found the money on their bodies, $10,000 apiece."
The deputy FM told CNN Israel would conduct an impartial investigation into the raid and would welcome the presence of foreign observers to ensure the probe's credibility.
Ayalon is set to depart for Europe on Monday. He is scheduled to meet ministers and state officials in Rome and Paris and is expected to urge both countries to impose European sanctions on Iran.
Earlier Sunday, Prime Minister Benjamin Netanyahu confirmed at a Likud ministers meeting that the Israeli investigation into the IDF flotilla raid will be headed by retired Supreme Court Justice Jacob Tirkel.
Netanyahu added that negotiations with the US over the establishment of an investigation committee, its composition, and the rights afforded it were held until late Saturday night, and that he expects an agreement on the matter shortly.