Others were thrown off the deck and landed in the water, the sergeant said. He saw another shot and spitting blood.
A commando identified only as "A" said that as they rappelled onto the deck, they were attacked, stripped of their equipment and weapons. At one point one of the passengers seized one of the soldiers' weapons and opened fire, he said.
Turkey's NTV showed activists beating one Israeli soldier with sticks as he descended from a helicopter onto the Mavi Mamara. Several passengers appeared to be bleeding and wounded in a report shown on Turkish television.
Video on a Turkish website showed pandemonium on board one of the ships, with activists in orange life jackets running around as some tried to help a colleague apparently unconscious on the deck. The site also showed video of an Israeli helicopter flying overhead and Israeli warships nearby.
At least three of the six ships were towed to the Israeli port of Ashdod. Some of the wounded had been taken to Israeli hospitals while others remained on a ship that had not yet arrived. Israeli officials said the people on board the ship would be processed at sea, and then deported.
A spokesman for the Israel foreign ministry said about 90 to 100 people were on the three ships already docked in Ashdod. About 25 of those people have agreed to be deported, but the others are refusing to identify themselves. Those refusing to cooperate hid their passports and some threw their passports into the sea, the spokesman said.
White House spokesman Bill Burton said the United States "deeply regrets the loss of life and injuries sustained." He said that administration officials are "currently working to understand the circumstances surrounding this tragedy."
The international reaction was more critical. The U.N. released a statement condemning the violence, and calling on Israel for "a full explanation."
"Such tragedies are entirely avoidable if Israel heeds the repeated calls of the international community to end its counterproductive and unacceptable blockade of Gaza," the statement read.
The violence also worsened Israel's relationship with Turkey, which had long been one of Israel's few friends in the Muslim world. Turkey announced that it was withdrawing its ambassador to Israel and demanded an emergency session of the U.N. Security Council.
The U.N. Security Council held an emergency session on the confrontation, hearing statements from the 15 council members as well as from Israel and the Palestinians. The council then went into closed consultations to consider possible action.
French President Nicolas Sarkozy released a statement condemning the "disproportionate use of force" and expressed his condolences to the families of the victims. France's Foreign Minister Bernard Kouchner said in a statement that "nothing can justify the use of such violence," and called for an investigation into the matter.
There were protests against Israel in Istanbul, London, Karachi, and Cairo. In Jerusalem today, government spokesmen were in "damage limitation mode."
Palestinian President Mahmoud Abbas described the incident as a massacre and has called for three days of mourning. Israeli police are on high alert in case of any retaliation.
The Associated Press contributed to this report