Israel said the forces encountered unexpected resistance as they boarded the vessels. Dozens of passengers and at least five Israeli soldiers were wounded in the confrontation in international waters.
Israel's tough response triggered widespread condemnation across Europe; many of the passengers were from European countries. The raid also strained already tense relations with Israel's long-time Muslim ally Turkey, the unofficial sponsor of the mission, and drew more attention to the plight of Gaza's 1.5 million people.
Turkey announced it was withdrawing its ambassador to Israel, cancelling three joint military drills and calling on the UN Security Council to convene in an emergency session about Israel. The Israeli ambassadors in Sweden, Spain, Denmark and Greece were summoned for meetings, and the French foreign minister called for an investigation.
The violent takeover also threatened to deal yet another blow to Israel's international image, already tarnished by war crimes accusations in Gaza and its blockade of the impoverished Palestinian territory.
It occurred a day before Prime Minister Benjamin Netanyahu was to meet with President Barack Obama at the White House to discuss the Middle East peace process.
French President Nicolas Sarkozy condemned "the disproportionate use of force" against the flotilla.
"All light must be shed on the circumstances of this tragedy, which underlines the urgency of resuming peace talks," he said in a statement.
Israeli Defence Minister Ehud Barak expressed regret for the deaths but blamed the violence on organisers of the flotilla, calling the effort a "political provocation" by anti-Israel forces.
Israeli security forces were on alert across the country, and the government advised Israelis to avoid travel to Turkey.
There were conflicting accounts of what happened early today.
An Al-Jazeera reporter on one of the Turkish ships said the Israelis fired at the vessel before boarding it. The Israelis, who had declared they would not let the ships reach Gaza, said they only opened fire after being attacked by activists with sticks, knives and live fire from weapons seized from the Israeli commandos.
"On board the ship we found weapons prepared in advance and used against our forces," declared Israel's deputy foreign minister, Danny Ayalon.
"The organisers' intent was violent, their method was violent and the results were unfortunately violent. Israel regrets any loss of life and did everything to avoid this outcome."
Palestinian President Mahmoud Abbas condemned the Israeli "aggression," declared three days of mourning across the West Bank and called on the UN Security Council and Arab League to hold emergency sessions on the incident.
Ismail Haniyeh, leader of the rival Hamas government in Gaza, condemned the "brutal" Israeli attack and called on UN Secretary-General Ban Ki-moon to intervene.
Israel's military chief, Lt. Gen. Gabi Ashkenazi, said soldiers were forced by violent activists to respond with live fire.
The activists were headed to Gaza on a mission meant to draw attention to a three year-old Israeli blockade of the coastal territory. Israel imposed the blockade after Hamas, which it considers a terrorist group, violently seized the territory.
The Israeli military said troops only opened fire after encountering unexpected resistance from the activists. Activists attacked troops with knives and iron rods, and opened fire with two pistols seized from the forces.
A total of five soldiers were wounded, two seriously, including at least one hit by live fire, the army said. Two of the dead activists had fired at soldiers with pistols, the army said.
"They planned this attack," said Israeli military spokeswoman Lt. Col. Avital Leibovitch. "Our soldiers were injured from these knives and sharp metal objects ... as well as from live fire."
The ships were being towed to the Israeli port of Ashdod, and wounded were evacuated by helicopter to Israeli hospitals, officials said. One of the ships had reached port by midday.
There were no details on the identities of the casualties, or on the conditions of some of the more prominent people on board, including 1976 Nobel Peace Prize laureate Mairead Corrigan Maguire of Northern Ireland, European legislators and Holocaust survivor Hedy Epstein, 85.
The United Nations expressed "shock" and condemned the killings. "We are in contact with the Israeli authorities to express our deep concern and to seek a full explanation," said a statement from the highest-ranking UN official in the region, Robert Serry.
Netanyahu later spoke by telephone with top Israeli officials and expressed his "full backing" for the military, according to a statement from the army.
The White House said in a written statement that the US "deeply regrets" the loss of life and injuries and was working to understand the circumstances surrounding this "tragedy."
An Israeli commando who spoke to reporters on a naval vessel off the coast said he and his comrades were surprised by a group of Arabic-speaking men when they rapelled onto the deck.
He said some of the soldiers, taken off guard, were stripped of their helmets and equipment and thrown from the top deck to the lower deck, and that some had even jumped overboard to save themselves. At one point one of the passengers seized one of the soldiers' weapons and opened fire.
A high-ranking naval official displayed a box confiscated from the boat containing switchblades, slingshots, metal balls and metal bats. "We prepared (the soldiers) to deal with peace activists, not to fight," he said. Most of the 10 dead were Turkish, he added.
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