Turkey withdrew its ambassador to Israel immediately after the raid, scrapped three joint military exercises and called the U.N. Security Council to an emergency meeting that demanded an impartial investigation.
Prime Minister Recep Tayyip Erdogan told lawmakers in the Parliament that the boarding of the Mediterranean flotilla was an attack "on international law, the conscience of humanity and world peace."
"Today is a turning point in history. Nothing will be same again," Erdogan said.
Turkey's Foreign Ministry said four Turkish citizens were confirmed slain by Israeli commandos and another five were also believed to be Turks, although Israeli authorities were still trying to confirm their nationalities.
"This bloody massacre by Israel on ships that were taking humanitarian aid to Gaza deserves every kind of curse," Erdogan said, demanding that Israel immediately halt its "inhumane" blockade of Gaza.
The flotilla was the ninth attempt by sea to breach the three-year-old blockade Israel and Egypt imposed after the militant Hamas group violently seized the Gaza Strip in 2007, home to 1.5 million Palestinians. Israel allowed five seaborne aid shipments to get through but snapped the blockade shut after its 2009 war in Gaza.
The United Nations Security Council Tuesdayinto Israel's actions. After an emergency meeting and marathon negotiations, the 15 council members agreed early Tuesday on a presidential statement that was weaker than that initially demanded by the Palestinians, Arabs and Turkey.
They had called for condemnation of the attack by Israeli forces "in the strongest terms" and "an independent international investigation."
Turkey's Deputy Prime Minister Bulent Arinc said Turkey would launch legal action at a Turkish court against Israel over the incident.
Erdogan said the Israeli raid proved "how good they are at killing people."
"Israel in no way can legitimize this murder, it cannot wash its hands of this blood," Erdogan said.
Turkey also demanded that the United States more strongly condemn the raid. Turkey's Foreign Minister Ahmet Davutoglu made the comments ahead of a meeting with U.S. Secretary of State Hillary Rodham Clinton.
The White House has reacted cautiously to the raid, calling for the disclosure of the full facts.
Davutoglu told reporters: "I have to be frank, I am not very happy with this statement from Washington yesterday."
He added: "We expect a clear condemnation."
According to the statement released by the Security Council, the U.N. wanted a "prompt, impartial, credible and transparent investigation conforming to international standards."
The Security Council's unanimous "presidential statement" also called for the "immediate release of the ships as well as the civilians held by Israel." CBS News foreign affairs analyst Pamela Falk at the U.N. says a "presidential statement," though not as strong as a full U.N. resolution, is a powerful message.
"The U.S. delegation succeeded in tempering the language of the Security Council statement introduced by Lebanon and Turkey, which initially had language condemning Israel and calling for a U.N. investigation," said Falk.
Erdogan said Turkey would continue to support the Palestinian people.
"We will not turn our back on Palestine, Palestinians and Gaza," Erdogan said.
"No one should test Turkey's patience," he added. "Turkey's hostility is as strong as its friendship is valuable."
He urged Israelis to question the actions of their government.
"It is damaging your country's image by conducting banditry and piracy," Erdogan said. "It is damaging interests of Israel and your peace and safety. It is the Israeli people who must stop the Israeli government in the first place."
He said Israel cannot face the international community without expressing "regret."
"Israel cannot ensure its security by drawing the hatred of the entire world," the prime minister declared.
Turkey sent three planes to bring back some 20 Turks wounded during clashes that broke out when Israeli commandos raided the Turkish vessel. Erdogan said he had snubbed an Israeli offer to fly back the Turkish wounded.
The nationalities of the dead have not been released yet.
Turkey has been increasingly assertive diplomatically in the Middle East. It has also accused Israel of abandoning Turkish-mediated talks with Syria, which demands the full withdrawal of Israeli troops from the Golan Heights as a condition for peace.
Meanwhile, another large cargo ship, the MV Rachel Corrie, had left port in Ireland and was sailing toward Gazan waters Tuesday.
Dr. Arafat Shoukri, Director of the Council for European-Palestinian Relations, a partner in the "Free Gaza" aid operation, told CBSNews.com the Corrie was still three days away from the Middle East and that the flotilla's organizers "have not decided yet" whether it should continue on its path.
"We will decide in the coming two days," Shoukri told CBS.
He said he was "sure" any any activists who engaged in violence against Israeli troops Monday did so "in self defense". Shoukri said his organization doesn't believe the Security Council's condemnation of the "acts" goes far enough. "It should be stronger," he told CBS in a phone interview.
Asked whether the roughly 20 people - mostly European nationals - aboard the Corrie were in any way armed or braced for clashes with Israeli Defense Forces, Shoukri said: "This is a humanitarian mission ... In no way are they prepared to confront the Israeli military."
CBS News Tel Aviv bureau chief Gaby Silon reports that about 50 foreigners from the ships were brought to an airport detention center in Israel Tuesday, waiting for deportation. Their nationalities were unclear but it didn't seem that American nationals were among those at the airport.
U.S. Embassy officials had been to the port detention center in Ashdod to speak with Americans detained in the raid. The officials would not tell CBS News how many Americans were present.
All Americans were to be deported as soon as bureaucratic procedures were completed, according to the Embassy officials.
Silon reports that Israeli officials were expected to truck much of the aid material brought to the country by Monday's bloodied flotilla into Gaza on Tuesday.
Silon reports that, despite fear of widespread unrest from the Arab population in Israel, the West Bank and Arab villages and towns remained relatively quiet Tuesday morning. Some strikes and demonstrations were planned for later in the day.