The raid, in which at least 10 pro-Palestinian activists were killed, was a new blow to Israel's international standing at a time when the West -- including the United States -- have grown frustrated with its stance in the peace process. The bloodshed particularly hurts its relations with Turkey, which was once a close regional ally of Israel but has become increasingly critical of it.
Around 10,000 Turks marched in protest from the Israeli consulate in Istanbul to a main square, chanting, "Murderous Israel you will drown in the blood you shed!" The protesters earlier tried to storm the Consulate building but were blocked by police. The flotilla of six ships, carrying some 700 activists, was sponsored in part by a Turkish organization.
Around 1,000 protested in Jordan's capital, Amman, calling for their government to cut diplomatic ties with Israel. Smaller protests erupted in capitals across the Middle East as well as in the Bosnian capital Sarajevo, the Greek city of Thessaloniki and the Pakistani city of Karachi.
Palestinian youths protesting the raid scuffled with Israeli soldiers, throwing bottles and stones at them, at a checkpoint north of Jerusalem, as senior Palestinian negotiator Saeb Erekat called the Israeli raid a "war crime."
Israel says the activists attacked its commandos as they boarded the six ships taking tons of supplies to Gaza, while the flotilla's organizers say the Israeli forces opened fire first.
U.N. Secretary-General Ban Ki-moon condemned the violence, saying, "I am shocked by reports of killing of people in boats carrying supply to Gaza. I heard the ships were in international water. That is very bad." He called for a "thorough investigation."
The White House issued a cautious reaction, saying "The United States deeply regrets the loss of life and injuries sustained, and is currently working to understand the circumstances surrounding this tragedy."
The European Union's foreign affairs chief, Catherine Ashton, said the bloc was deeply concerned and she called on Israel to carry out an inquiry.
French President Nicolas Sarkozy condemned "the disproportionate use of force" against the flotilla.
"All light must be shed on the circumstances of this tragedy, which underlines the urgency of resuming peace talks," he said in a statement.
Greece suspended a military exercise with Israel and postponed a visit by Israel's air force chief. Greece, Egypt, Sweden, Spain and Denmark summoned Israel's ambassadors demanding explanations for the violence.
But the strongest reaction came from Turkey. Deputy Prime Minister Bulent Arinc called Israel's actions "piracy" and said Turkey is withdrawing its ambassador on Monday as well as canceling three joint military drills and calling on the U.N. Security Council to convene in an emergency session about Israel. Turkey is currently a member of the council.
"I strongly condemn the use of force by Israeli military forces on an aid convoy composed of 32 countries, including Turkey," Arinc said. "This attack must not remain unanswered." He also said a Turkish youth soccer team currently in Israel would be brought home.
The raid also brought heightened attention to Israel's blockade of the Gaza Strip, imposed after the Palestinian militant group Hamas seized control of the tiny Mediterranean territory in 2007. The blockade -- along with Israel's fierce offensive against Gaza in the winter of 2008-2009 to stop Hamas rocket fire -- has fueled anti-Israeli sentiment around the Arab world.
The president of Iran, a key supporter of Hamas, called the raid "an inhuman act."
"All in all, these (actions) only bring closer the end of the miserable and false regime" in Israel, President Mahmoud Ahmadinejad said, according to state TV.
The Cairo-based Arab League called an emergency session for Tuesday to address the attack, as the two only Arab states with peace deals with Israel -- Jordan and Egypt -- sharply condemned the violence. Jordan's information minister, Nabil al-Sharif, called it a "heinous crime" and called for the lifting of the blockade on Gaza.
The incident also put Egypt in a tight position. The only Arab country bordering the Gaza Strip, it has helped enforce the blockade by cracking down on smuggling tunnels that are a key source of goods to Gaza's 1.5 million people and by rejecting pressure that it open its border crossing. The Egyptian government has said it cannot open the border since there is no agreement on restoring European monitors who left during the Hamas takeover.
Egypt's Foreign Ministry said the violence underlines how Gaza "remains under total Israeli occupation," and it called "for the immediate lifting of the Israeli siege on Gaza."
In Beirut, about 500 Palestinian and Lebanese activists protested in front of the U.N. headquarters, setting Israeli flags on fire. "The only solution with the usurping entity is resistance. This entity only understands the language of force," Hezbollah lawmaker Nawar al-Saheli told the crowd.
In neighboring Syria, more than 200 Syrian and Palestinian protesters staged a sit-in before the offices of the United Nations to denounce the Israeli raid.