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Israel's Channel 10 TV said 19 passengers were killed and 36 wounded in the raid.
A Turkish charity said, at least 15 people were killed, most of them Turkish nationals.
Turkey said it had called for an emergency meeting of the U.N. Security Council after the attack, a Turkish foreign ministry official said.
Turkey is a non-permanent member of the Council.
Israeli Ambassador in Ankara Gaby Levy was summoned to the Ministry of Foreign Affairs after Israeli navy raided a convoy of six ships carrying civilians and humanitarian aid to Gaza.
At his meeting with the Israeli ambassador, Deputy Undersecretary Unal Cevikoz conveyed Turkey's protest and said that the attack was totally unacceptable.
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"Down with Zionist, Israeli imperialism," protesters shouted as police backed by armoured vehicles and water cannon barred them from moving towards the building.
Other chants called for Turkey to send troops to Gaza and for the Turkish ships to be released.
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Protestors threw eggs and plastic bottles at the garden of residence.
The group is still in front of the residence of Levy, shouting slogans against Israel.
"Once again"
The Human Rights and Freedoms (IHH) Humanitarian Aid Foundation, which carries out the aid campaign, said that Israeli troops boarded the ship from a helicopter and boats and opened fire.
The foundation established a crisis desk, and said that there were about 800 passengers including a six-month-old baby on board the ships intercepted by Israeli navy. The foundation added that they lost communication with the ships.
Turkey's Foreign Ministry released a statement and strongly condemned Israeli navy's interception.
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After release of the statement, Israeli Ambassador in Ankara Gaby Levi was summoned to the Ministry of Foreign Affairs.
The Turkish party protested the attack and told the Israeli ambassador, "it is against the international law to intercept ships, which sail in the international waters and carry humanitarian aid, by using force. It is impossible to accept and tolerate such an interception."
"Preserving our rights"
Turkey requested detailed report about fate of passengers of the international convoy including citizens from 33 countries.
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The interception also topped agenda of an extraordinary meeting held at the Prime Ministry Office under the chairmanship of Deputy Prime Minister Bulent Arinc.
According to the Israeli Ynet news portal, Israeli Defense Minister Ehud Barak called Turkish Foreign Minister Ahmet Davutoglu and National Defense Minister Vecdi Gonul. Barak also met with the Turkish ambassador in Tel Aviv.
"Attack on international waters"
Turkey's Maritime Undersecretary Hasan Naiboglu said, "the ships, 'Gaza', 'Blue Marmara' and Defne Y' headed for Palestine without entering territorial waters of Israel. Captain of the Blue Marmara called us at around 4:30 a.m. and told us that Israeli navy intercepted them. We learnt that there were a number of injured people. Then, we lost contact with the ships. We think that the ships were diverted to the Israeli port of Ashdod," he said.
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The Palestinian Embassy in Ankara and the Jewish Community in Turkey reacted to the raid.
The Palestinian Embassy said in a statement, "we condemn barbarous attack by Israel on the aid ships. The attack is an organized state terrorism against civilians coming all around the world to help oppressed people living under besiege more than four years. This is a barbarous attack against our people living in Gaza, human rights, and NGOs which defend international laws and organized this convoy."
The Chief Rabbi's Office said, "we have learned with great sorrow about the military intervention against Mavi Marmara ship which was headed towards Gaza. The news reports saying there are casualties further deepened our sorrow. We share the protests in our country incurred by the intervention and share our sorrows with the public."
"Call for UN meeting"
Turkey has called for an emergency meeting of United Nations Security Council after Israeli operation on a convoy carrying humanitarian aid to Gaza on Monday.
Diplomatic sources said that Turkish Foreign Minister Ahmet Davutoglu cancelled his meetings in Washington, D.C. and would proceed to New York for UN Security Council meeting. Turkey is a non-permanent member of the Council.
The convoy was organised, among others, by IHH.
Turkey had urged Israel to allow it safe passage and said the 10,000 tonnes of aid the convoy was carrying was humanitarian.
Deputy Prime Minister Bulent Arinc chaired an emergency meeting with Prime Minister Erdogan and Foreign Minister Ahmet Davutoglu to discuss the Turkish response.
Turkish Parliament Speaker Mehmet Ali Sahin said Monday that the Turkish parliament could issue a declaration to condemn Israeli raid.
Sahin strongly condemned the Israeli interception of the aid convoy.
"The Turkish parliament will give the necessary reaction in the face of this vicious attack. Our parliament can issue a declaration to condemn it," he added.
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"War should be our response," he said. "Our reaction has to be tougher than what the Israelis did to these innocent people." After reading verses from the Holy Qur'an, the protestors made a call on all to boycott Israeli products and services.
Speaking at the Taksim Square, a member of the IHH Executive Board Omer Faruk Korkmaz said that the Foundation fulfilled its duty and lost lives while trying to provide humanitarian assistance.
It is now high time for governments of the world to interfere in the issue, Korkmaz also said.
The flotilla, which includes three cargo ships and three passenger ships, is trying to draw attention to Israel's three-year blockade of the Gaza Strip. The boats are carrying items such as electric-powered wheelchairs, prefabricated homes and water purifiers.
World Bulletin