Nine activists were killed when Israeli troops raided one of the ships in an operation widely criticised by Turkey, which recalled its ambassador in protest, and others.
"This was not a love boat, this was a boat of hate," Mr Netanyahu said.
A mass deportation of foreign activists by air is under way.
As activists accused Israeli forces of brutality, the Geneva-based UN Human Rights Council voted to set up an independent international inquiry into the raid.
In London, UK Prime Minister David Cameron said Israel's raid was "completely unacceptable" and called for the Israeli blockade of Gaza to be lifted.
The International Quartet's Middle East envoy, former UK Prime Minister Tony Blair, said the blockade was "counter-productive".
"What [Israel] should be doing is allow material in to rebuild homes and sanitation and power and water systems, and allow business to flourish," he told Reuters news agency in an interview in Bethlehem.
The Israeli prime minister, who visited injured commandos in hospital in Tel Aviv on Tuesday, said the soldiers had been met by a "vicious mob" and had acted to defend themselves.
He said that it was Israel's duty to prevent rockets and other weapons being smuggled into Gaza to Hamas by Iran and others.
The flotilla, he argued, was not aiming to deliver humanitarian aid to Gazans but was trying to break the blockade.
Israel would not allow Gaza to become an "Iranian port in the Mediterranean", he said.
He dismissed criticism of the raid as "an attack of international hypocrisy".
"I regret to say that for many in the international community no evidence is needed: Israel is guilty until proven guilty," he remarked.
Earlier, Israeli Defence Minister Ehud Barak thanked the commandos involved in the raid when he visited them at their base in Atlit.
"We live in the Middle East, in a place where there is no mercy for the weak and there aren't second chances for those who don't defend themselves," he was quoted by Haaretz newspaper as saying.