Its report said the action by commandos, which left nine dead, was "disproportionate" and "betrayed an unacceptable level of brutality".
It said there was clear evidence to support prosecutions against Israel for "wilful killing".
Israel rejected the report as "biased" and "one-sided."
It insists its soldiers acted in self-defence during the 31 May raid.
Nine Turkish pro-Palestinian activists were killed and many others injured after Israeli commandoes boarded the six-ship convoy as it tried to breach an Israeli naval blockade of Gaza.
The convoy's passengers were detained and later deported by Israel.
There was widespread international criticism of Israel's actions, which severely strained relations with its long-time Muslim ally, Turkey.
In a 56-page report, the UN Panel of three international lawyers said: "There is clear evidence to support prosecutions of the following crimes within the terms of article 147 of the Fourth Geneva Convention: wilful killing; torture or inhuman treatment; wilfully causing great suffering or serious injury to body or health".
The Convention is an international treaty governing the protection of civilians in times of war.
The UN Human Rights Council report also said the Israeli blockade of the Palestinian territory was "unlawful" because of a humanitarian crisis there.