The sharply critical report found there was "clear evidence to support prosecutions" against Israel for "wilful killing" and torture committed in the raid on the flotilla on May 31. Nine activists on a Turkish ship were killed as they attempted to breach the Israeli naval blockade of Gaza.
However, Israel brushed aside the findings of the UN Human Rights Council, which it has consistently denounced as biased against the Jewish state.
A spokesman for the Israeli foreign ministry accused the body of having a "politicised and extremist approach," adding: "The Human Rights Council blamed Israel prior to the investigation and it is no surprise that they condemn after."
The investigation mounted by the Council has largely been superseded by a separate inquiry launched by Ban Ki-Moon, the UN secretary general, which has won the backing of the United States, Britain and much of the international community.
This investigation, which is being headed by Geoffrey Palmer, the former prime minister of New Zealand, has yet to report its findings.
In an unprecedented move, Israel agreed to co-operate with Mr Palmer's inquiry in August, largely in an attempt to diminish the credibility of the Human Rights Council investigation.
Israel maintains that its soldiers acted in self-defence after coming under attack from activists wielding clubs, axes and metal rods.
However the report found that Israeli commandos' response to the flotilla was disproportionate and "betrayed an unacceptable level of brutality".
"The conduct of the Israeli military and other personnel towards the flotilla passengers was not only disproportionate to the occasion but demonstrated levels of totally unnecessary and incredible violence," the report said.
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"The circumstances of the killing of at least six of the passengers were in a manner consistent with an extralegal, arbitrary and summary execution," it added.
The 56-page report also said that the Israeli blockade was itself unlawful, because of the humanitarian crisis in Gaza, meaning Israel's claim that it was entitled to use force to defend the blockade should be dismissed.
The Human Rights Council, a subsidiary body of the UN General Assembly, has courted controversy for its excessive focus on the Israeli-Palestinian conflict.
While it has passed over a dozen resolutions condemning Israel since it was created in 2006, the council has been more reluctant to censure states such as Sudan, which has been accused of serious human rights violations in Darfur.
The United States withdrew from the council in 2008 but rejoined when President Barack Obama became president last year.
Israel, which has also launched its own domestic inquiry into the raid on the aid flotilla, refused to co-operate with the council's probe.
But Hamas, the Islamist group which controls Gaza, welcomed the inquiry's findings and called on the international community to take action by bringing Israeli commanders involved in the raid to trial.
The inquiry was completed by Karl Hudson-Phillips, a former judge of the International Criminal Court in The Hague, Desmond de Silva, a former chief prosecutor of the Sierra Leone War Crimes Tribunal, and Shanthi Dairiam, as Malaysian human rights expert.