But he said soldiers had been arresting themselves afterwards they were "clubbed, baffled and stabbed".
Pro-Palestinian campaigners say the soldiers opened blaze assumed back they landed on the aid-carrying ships.
There has been all-embracing accusation of the accident of life, and the UN is captivation an emergency session.
As the affair of the UN Security Council got beneath way in New York, diplomats said the abstract argument of a resolution alleged for accusation of the operation, the actual absolution of the impounded ships and for an all-embracing inquiry.
Turkish Foreign Minister Ahmet Davutoglu alleged the adventure "murder committed by a state" and said Israel had "lost all legitimacy".
But Israeli UN adumbrative Daniel Carmon told the Security Council that some on lath the ships had motives added than accouterment altruistic assistance, and had approved to lynch Israeli soldiers.
Mr Netanyahu cut abbreviate a appointment to Canada to accord with the growing crisis and annulled a appointed affair in Washington with US President Barack Obama on Tuesday.
Israel imposed a barricade on the Gaza Strip afterwards the Islamist movement Hamas took ability there in 2007.
The six-ship accompany had set out to backpack 10,000 tonnes of aid from Cyprus to Gaza, admitting again Israeli warnings that it would not be accustomed to ability the territory.
In a statement, Mr Netanyahu dedicated the Israeli operation, adage troops were attacked back they landed on the better of the six ships in the flotilla.
"They were mobbed. They were clubbed, they were beaten, stabbed," he said.
"There was alike a address of battery and our soldiers had to avert themselves, avert their lives or they would accept been killed.
"Regrettably, in this exchange... bodies died. We affliction this accident of life. We affliction any of the violence."
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Organisers of the accompany accept acerb denied the Israeli account.
Contact with activists on the ships was absent afterwards the raids and no contiguous accounts from them accept yet emerged.
Arafat Shoukri, of the Free Gaza Movement (FGM) which helped organise the convoy, said those on lath one address had told them by blast that Israeli helicopters had arrived.
"Then we started to apprehend screams, shouting, cutting everywhere," he said. "We heard some of them shouting 'We are adopting the white flag, stop cutting at us'."
He said Israeli claims that activists had pistols and added weapons were "cheap propaganda".
Audrey Bomse, additionally of the FGM, told the BBC that the activists were "not activity to affectation any agitated resistance".
The fleet larboard the bank of Cyprus on Sunday and had been due to access in Gaza on Monday.
Reports say troops boarded the address about 40 afar (64 km) out to sea in all-embracing waters.
Organisers of the fleet said at atomic 30 bodies were blood-soaked in the incident. Israel says 10 of its soldiers were injured, one seriously.
There has been boundless accusation of the violence, with several countries summoning their Israeli ambassadors.
UN arch Ban Ki-moon said he was "shocked" and alleged for a "full investigation" into what happened.
The White House said the US "deeply abjure the accident of life" and was "currently alive to accept the affairs surrounding this tragedy".
There was a decidedly able acknowledgment from Turkey, area abounding of the activists on the ships are from.
Turkish Prime Minister Recep Tayyip Erdogan accused Israel of accompaniment agitation and abuse of all-embracing law.
In Istanbul, bags of protesters took allotment in an affronted affirmation adjoin Israel.
Turkey was Israel's abutting Muslim accessory but relations accept attenuated in contempo years.
Greece has aloof from collective aggressive contest with Israel in beef at the arrest on the flotilla.
The appointment of French President Nicolas Sarkozy said he accursed "the asymmetric use of force", while UK Foreign Secretary William Hague said there was "a bright charge for Israel to act with abstemiousness and in band with all-embracing obligations".
The BBC's Jon Donnison in Gaza says there has been boundless acrimony there with protests organised by Hamas.
Israel has escorted the ships to the anchorage of Ashdod and says it will deport the cartage from there.
Israel says it allows about 15,000 tonnes of altruistic aid into Gaza every week.