"These murderous attacks are characteristic tools used by Israel to derail every peaceful effort and silence every voice of moderation and reason,"
Pakistani ambassador Zamir Akram told the council on behalf of the Organisation of the Islamic Conference (OIC).
Describing the assault as a "heinous attack," Turkey's envoy stressed that "treating humanitarian aid delivery as a hostile act and aid workers as combatants is totally unacceptable."
Israeli ambassador Aharon Leshno Yaar, defending the military action, outlined international law and said the soldiers acted in self defence and only used live ammunition because they were attacked.
"The people who surrounded them were not peace activists, they were a lynch mob," said Yaar.
"Under applicable international law, capture of a vessel attempting to breach a naval blockade can be done in international waters, before entrance to the blockaded area," he added.
States from the Arab League and the OIC had asked for the special session of the 47 member state council.
Pakistan, Sudan and the Palestinian delegation also tabled a draft resolution for the debate seeking condemnation of the raid and aiming to set up an international inquiry.
The draft, which is to be submitted to a vote by the council on Wednesday, called for an "independent international fact-finding mission to investigate violations of international law resulting from the Israeli attacks on the flotilla of ships carrying humanitarian assistance."
It also "condemns in the strongest terms possible the outrageous attack by Israeli forces" and called for the release of all those detained in Monday's operation.
On Tuesday, Israel began the process of deporting more than 600 pro-Palestinian activists who were brought ashore after the deadly navy raid.
Israel warned Tuesday it would prevent all aid ships from reaching besieged Gaza, as activists vowed a new attempt to defy the three-year-old blockade of the Hamas-run Palestinian territory.
UN High Commissioner for Human Rights Navi Pillay had condemned Israel's use of military force as disproportionate, as the incident sparked widespread criticism when the council began its latest two week session on Monday.
"The blockade lies at the heart of so many of the problems plaguing the Israel-Palestine situation, as does the impression that the Israeli government treats international law with perpetual disdain," she said.
The UN Security Council in New York later called for an impartial investigation into the attack and the immediate release of all civilians.
A similar special session early last year led to a UN human rights investigation into Israel's 2008-2009 military offensive in the Gaza Strip.
The fact-finding mission led by former international war crimes prosecutor Richard Goldstone concluded that both Israel and Gaza's Hamas rulers committed war crimes and possible crimes against humanity.
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