After more than a decade of secrecy, Israel has confirmed it has conducted a 2007 military raid on what was believed to be a Syrian nuclear reactor.

The Israeli army said a total of eight F-16 and F-15 fighter jets bombed a Syrian nuclear facility in Deir Az Zor, 450km north of Damascus, in a stealth operation that lasted four hours overnight on September 5 to 6, 2007.

The attack, dubbed "Out of the Box" by Israel's military command, was long known to have occurred but was kept under an 11-year gag order forbidding Israeli media to publish details on the operation.

"The message from the attack on the nuclear reactor in 2007 is that the State of Israel will not allow the establishment of capabilities that threaten Israel's existence," said Israeli army chief of staff Gadi Eizenkot.

"This was our message in 2007, this remains our message today and will continue to be our message in the near and distant future," he added.

It is unclear why the army chose to disclose the information now.

Some speculate it could be a warning to Iran or be timed to coincide with the release of a memoir of Ehud Olmert, who served as prime minister during the raid.

Israeli daily Haaretz wrote that the operation was Olmert's "finest hour", who - just a year earlier - "had led Israel into a failed war in Lebanon and who less than two years later would be compelled to resign before going on to serve a prison term for crimes of corruption".

In 2011, the head of the International Atomic Energy Agency (IAEA), Yukia Amano, said for the first time that the target destroyed by Israeli warplanes was the covert site of a future nuclear reactor.

Amano's comments countered assertions by Syria that it had no atomic secrets, and it was the first time the UN nuclear watchdog spoke unequivocally about the issue.

"The facility that was ... destroyed by Israel was a nuclear reactor under construction," Amano said.

Previous reports by the IAEA only suggested that the structure could have been a nuclear reactor. In a February report, Amano said that features of the bombed structure in al-Kibar were "similar to what may be found at nuclear reactor sites".

After the bombing, Syria's refusal to allow IAEA inspectors access to the bombed site heightened suspicions that it had something to hide, along with its decision to level the destroyed structure and later build over it.

Drawing on the 2008 visit by its inspectors, the IAEA determined that the destroyed building's size and structure fit specifications that a reactor would have had. The site also contained graphite and natural uranium particles that could be linked to nuclear activities.

The IAEA had tried to probe several other sites for possible undeclared nuclear activities linked to the bombed target. But the Syrian government said most of the sites were restricted because of their military nature.