Israel's right-wing government has been on the defensive on several fronts since taking office in early 2009.
It has been under pressure from the US to rein in settlement expansion to promote fledgling peace talks with the Palestinian Authority, and the United Nations's Goldstone panel has accused the Israeli army of carrying out war crimes against Gaza civilians in a three-week offensive to snuff out Hamas rocket fire.
Defense Minister Ehud Barak called on world leaders to exercise restraint in their response to the incident.
"The entire flotilla is a political and media provocation by anti-Israeli activists," said Defense Minister Ehud Barak at a press conference in Tel Aviv. "They have absolutely nothing to do with humanitarian aid."
Israeli officials said that when the flotilla ignored calls from its naval forces to respect its closure of Gaza's territorial waters, soldiers boarded the ships from helicopters and from naval sea craft. The army said commandos encountered unexpectedly violent resistance from activists armed with knives, metal clubs, and live weapons on the Marmara, a ship with 600 activists.