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Evan Kohlmann, a terrorism analyst at the NEFA Foundation, said in an interview that he doubted the group has ties to al Qaeda, but that the charity had a history of support for jihadist organizations.

“This purported charity is a fairly extreme organization,” he said. “It has associated itself with a number of political viewpoints which are not only fairly militant but they seem to fall well outside of what one would normally expect from a humanitarian group.”

Mr. Kohlmann said the group, which was formed in 1995 in protest of the Serbian attacks on Muslims during the disintegration of Yugoslavia, was initially involved in the recruitment of jihadist fighters.

“In the 1990s, Turkish authorities acquired evidence that IHH was involved in not just humanitarian fundraising, but also recruiting fighters for conflicts in the Muslim world,” Mr. Kohlmann said. “A search by the Turkish authorities of the IHH offices in Turkey turned up weapons and hard-core jihadist propaganda.”

Izzet Sahin, a spokesman for IHH, told the Associated Press on Monday that his organization had no ties to terrorism and denied the Israeli charges.

The U.S. reaction was mild compared with that of other allies of Israel. A statement from India’s External Affairs Ministry said, “India deplores the tragic loss of life and the reports of killings and injuries to the people on the boats carrying supplies for Gaza. There can be no justification for such indiscriminate use of force, which we condemn.”

Russia, Egypt and Britain also condemned the incident.

Street protests against Israel were held in Turkey, Iran, Egypt, Pakistan, Jordan, France, England, Greece and Spain. In Istanbul, protesters burned a Star of David. Protests also were held in New York.

Aaron David Miller, a former U.S. Middle East peace negotiator, said the incident was bad for Israel on many levels.

“This feeds the efforts of those in the international community who seek to delegitimize Israel. This has undermined Mahmoud Abbas, who will have to toughen his position in negotiations or even suspend them. This hands Hamas a huge political windfall,” he said.

Mr. Miller, who is now a scholar at the Woodrow Wilson International Center for Scholars, added that the incident “calls into question the competency and judgment of the Israeli security establishment who obviously explored a number of options.” He added, “If I were this free Gaza movement, I would be sending these boats every week.”

This article is based in part on wire service reports.