Asked about the existence of any such agreement at a New York press conference, Ban said none had been created "behind the scenes".
Israel responded firmly to Ban's denial, with Prime Minister Benjamin Netanyahu reiterating that "Israel would not participate in any panel which wants to question IDF soldiers."
A source in Jerusalem claimed that according to earlier agreements between Israel and the UN secretary general, the UN commission would base itself on reports from Israeli and Turkish commissions.
The same senior source said any request for further information or clarification from Israel or Turkey would be given only via sources appointed by those two states.
He added that the issue had been made clear to Ban before Israel agreed to the commission, and that Israel had said it would not permit any access to or investigation of IDF soldiers by the panel. "This was and remains a critical condition for Israel's participation," Jerusalem said in response to Ban's denial.
The UN chief was speaking ahead of the first meeting of the international inquiry committee, which includes former prime minister of New Zealand, Geoffrey Palmer, outgoing Colombian President Alvaro Uribe, and representatives from Israel and Turkey.
Ban told the conference he would meet officially with the team on Tuesday, and expressed hope that its work would contribute to "regional stability".
Regarding the panel's mandate, Ban said it would be required to examine and identify the facts, circumstances, and context of the raid on the Gaza-bound Marmara in May, which killed nine Turkish activists.
He added that the committee would be asked to recommend methods of preventing such incidents from occurring in the future, and that it would have to determine steps necessary for cooperation with Turkey and Israel as the inquiry develops.
The UN chief said he had demanded the panel's first report by mid-September, before the UN General Assembly convenes.
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