Israel National News has a harrowing first-hand report from one of the naval commandos:

Fiamma Nirenstein reports:

"At four in the morning, a firsthand witness Carmela Menashe, a military reporter who mercilessly uncovered many scandals in the Israeli army, declared that when soldiers from the Israeli Navy tried to get off the ship they were welcomed with gunfire. 'There were firearms on the ship' of the pacifists; the soldiers that touched the bridge faced a lynching 'like that of Ramallah' in which human limbs were thrown into the crowd. They used, with enormous impetuosity according to recounts, iron bars, knives and gas. The Israeli soldiers were thrown into the hold of the ship by the 'pacifists' in an attempt to either kidnap or throw them into the sea. This explains why their mates fired. Of course, the sailors were not part of a military, they were civilians: but, by now, in asymmetric warfare civilians are used as human shields and combatants."

Here is an official statement from Israeli Ambassador to the US Michael Oren.