Six civilian ships of the Gaza Freedom Flotilla were raided by Israel on 31 May 2010 in international waters in the Mediterranean Sea. Nine of the flotilla passengers were killed during the raid, with 30 wounded (including one who later died of his wounds). Ten Israeli soldiers were wounded, one seriously. The exact sequence of events is contested, in part due to the IDF's confiscation of the passengers' photographic evidence. The flotilla, organized by the Free Gaza Movement and the Turkish Foundation for Human Rights and Freedoms and Humanitarian Relief (İHH), was carrying humanitarian aid and construction materials, intending to break the Israeli naval blockade of the Gaza Strip.

The Israeli Navy warned the flotilla via radio to stop approaching the naval blockade and to change course to the port of Ashdod. This request was denied and on 31 May 2010, Israeli Shayetet 13 naval commandos boarded the ships in international waters from speedboats and helicopters. Aboard the Turkish ship MV Mavi Marmara, the Israeli Navy faced resistance from about 40 of the 590 passengers, including IHH activists who were said to be armed with iron bars and knives. During the struggle, nine activists were killed, including eight Turkish nationals and one Turkish American, and many were wounded. On 23 May 2014, a tenth member of the flotilla died in hospital after being in a coma for four years. Ten of the commandos were also wounded, one of them seriously.

According to a United Nations Human Rights Council report, all activist deaths were caused by gunshots, and "the circumstances of the killing of at least six of the passengers were in a manner consistent with an extra-legal, arbitrary and summary execution." The five other ships in the flotilla employed passive resistance, which was suppressed without major incident. According to the UNHRC report, several of the passengers were injured and the leg of one was fractured. The ships were towed to Israel. Some passengers were deported immediately, while about 600 were detained after they refused to sign deportation orders; a few of them were slated for prosecution. After international criticism, all of the detained activists were also deported. The raid drew widespread condemnation internationally, resulted in a deterioration of Israel–Turkey relations, and Israel subsequently eased its blockade on the Gaza Strip.

There were several probes into the incident. A UNHRC report in September 2010 deemed the raid illegal and stated that Israel's actions were "disproportionate" and "betrayed an unacceptable level of brutality", with evidence of "wilful killing". United Nations Secretary-General Ban Ki-moon announced a parallel probe in August 2010 by a four-member panel headed by Geoffrey Palmer. The Palmer report was published in September 2011 and also concluded that the raid was illegal. The report stated that the degree of force used against the Mavi Marmara was "excessive and unreasonable", and that the way Israel treated detained crew members violated international human rights law. In response to the raid, Israel offered Turkey $20 million in compensation, which was discussed in March 2013, with an agreement finalized in June 2016.

The operation, code named Operation Sea Breeze or Operation Sky Winds was an attempt to block the Free Gaza Movement's ninth attempt to break the naval blockade imposed by Israel on the Gaza Strip. Israel proposed inspecting the cargo at the Port of Ashdod and then delivering non-blockaded goods through land crossings, but this proposal was turned down. Israeli forces then raided and seized the Gaza-bound ships in international waters of the Mediterranean.

The raid ended with nine activists killed, and dozens injured. A UNHRC fact-finding mission described six of the nine passengers' deaths as "summary execution" by the Israeli commandos. A BBC documentary concluded that Israeli forces had faced a violent premeditated attack by a group of hardcore IHH activists, who intended to orchestrate a political act to put pressure on Israel. The programme was criticised as "biased" by critics of Israel and the PSC (Palestine Solidarity Campaign) questioned why the IDF boarded the ship at night if it had peaceful intention. Seven Israeli commandos were injured in the skirmish. After seizing control of the ships, Israeli forces towed them to Ashdod and detained the passengers.

The raid prompted widespread international reactions and demonstrations around the world. The United Nations Security Council condemned "those acts resulting in civilian deaths", demanded an impartial investigation of the raid, and called for the immediate release of civilians held by Israel. Israel released all passengers of the flotilla by 6 June 2010. The incident threatened the already deteriorating relations between Turkey and Israel. Turkish president Abdullah Gül described the raid as an attack on Turkey for the first time since World War I.

Israel initially rejected calls from the United Nations and world governments for an international investigation into its raid on the Gaza aid flotilla, but later agreed to cooperate with an investigation conducted by the United Nations. Israel formed the Turkel Committee to investigate the raid. The committee, headed by retired Supreme Court of Israel judge Jacob Turkel, included two international observers.