"Ultimately we are sure that the facts are on our side," Mark Regev, the Israeli government spokesman, said.
"We have no problem whatsoever with a credible, objective panel."
Regev did not explain exactly how Israel planned to co-operate with the panel.
Israel had until now rejected calls for an international independent investigation into the commando raid and has shunned previous UN investigations into its military actions.
It refused to co-operate with a commission that accused it last year of suspected war crimes in the 22-day assault on the Gaza Strip, which killed 1,400 Palestinians and a dozen Israelis.
Ban Ki-moon, the United Nations secretary-general, said the panel would begin work on August 10, and would submit its first progress report by mid-September.
Turkey, which prior to the raid on the Mavi Marmara vessel had diplomatic ties with Israel, welcomed the UN inquiry as a "step taken in the right direction".
"It is imperative that the investigation is carried out in a swift, objective and transparent manner in line with international standards ... We believe all the panel members will act in an objective and responsible manner," a statement from the Turkish foreign ministry said.
Turkey hopes that the result of the inquiry will serve to "install respect for international law and contribute to preventing a repeat of similar violations".
Ankara recalled its ambassador and cancelled three planned joint military exercises with Israel after the raid. It says Israel must apologise, pay compensation for the victims and lift the blockade of Gaza for ties to be resumed.
The United Nations Human Rights Council named its own three-person flotilla commission last month. That panel is also expected to report its findings in September.
The Israeli army's internal inquiry into the raid recommended no disciplinary action against senior officers, and concluded that "the use of live fire was justified" on board the Mavi Marmara.
A separate civilian panel, chaired by former Israeli supreme court judge Jacob Turkel, is also investigating the raid.