Israel has long been assumed to have carried out the raid and had been named by other countries as being behind it, but it had never formally acknowledged the strike or divulged details.
The admission along with the release of newly declassified material related to the raid comes as Israel intensifies its warnings over the presence of its main enemy Iran in neighbouring Syria.
Netanyahu has also repeatedly called for a landmark 2015 nuclear deal between world powers and Iran to be changed or eliminated.
US President Donald Trump, who met Netanyahu at the White House this month, has said that the nuclear deal must be “fixed” by May 12 or the United States will walk away.
After Wednesday’s acknowledgement, Netanyahu said “the Israeli government, the (Israeli military), and the Mossad (intelligence agency) have prevented Syria from developing nuclear capability, and they deserve every credit for this.”
“Israel’s policy has been and remains consistent — to prevent our enemies from acquiring nuclear weapons.”
Intelligence Minister Yisrael Katz was more explicit, saying it showed Israel would never allow nuclear weapons to be obtained by “countries like Iran who threaten its existence”.
The declassified material includes footage of the strike and pictures of secret army intelligence communiques about the site.
A military statement lays out the case for why Israel carried out the strike at the desert site in the Deir Ezzor region of eastern Syria on what it says was a nuclear reactor under construction.
Syria has denied it was building a nuclear reactor.
“On the night between September 5th-6th, 2007, Israeli Air Force fighter jets successfully struck and destroyed a Syrian nuclear reactor in development,” the Israeli statement says.
“The reactor was close to being completed. The operation successfully removed an emerging existential threat to Israel and to the entire region — Syrian nuclear capabilities.”
– ‘Strategic implications’ –
In 2008, less than a year after the strike, US officials accused Syria of having sought to build a secret nuclear reactor and acknowledged Israel destroyed it in the raid.
The UN atomic watchdog declared in 2011 that the Syrian site was “very likely” to have been a nuclear reactor, adding that information provided to it suggested that it was being built with North Korean assistance.
Israel said in its new disclosures that secrecy surrounding the strike was necessary due to the sensitive security situation, noting there was the possibility of it provoking war.
In defending the strike, it notes that Islamic State group jihadists later overran much of Deir Ezzor during Syria’s civil war, while also saying that Syrian President Bashar al-Assad “in the past used chemical weapons against his own citizens.”
“The nuclear reactor being held by Assad would have had severe strategic implications on the entire Middle East as well as Israel and Syria,” it said.
While Israel’s admission will come as little surprise, the declassified material provides details on what is widely known as Operation Orchard.
The material speaks of an ultra-secretive operation, with few knowing details and a cover story provided.
Israeli intelligence had picked up on what it determined was the construction of the nuclear reactor and followed its development, it says.
Four F-16s and four F-15s were involved in the strike, with the operation beginning at 10:30 pm on September 5 and the planes returning at 2:30 am the following day.
Grainy footage of the strike included in the material shows a target locking on to a building that is blown apart shortly afterwards.
Israel determined that the alleged reactor was “totally disabled, and that the damage done was irreversible.”
Israeli armed forces chief of staff Lieutenant General Gadi Eisenkot, northern commander at the time, recalled in a video in the material meeting with his officers shortly before the raid.
“I don’t give them the exact details of the target and its essence, but I say that there’s going to be a significant attack in the upcoming 24-48 hours, an event that in low likeliness could lead to war,” he said.
“Low, to me, is even 15 or 20 percent, which is a lot.”
– ‘Message’ sent? –
Syria and Israel have fought in repeated wars since the Jewish state’s founding in 1948. The two countries are still technically at war.
Israel has sought to avoid direct involvement in the Syrian civil war that broke out in 2011, but it acknowledges carrying out dozens of air strikes there to stop what it says are advanced arms deliveries to Lebanese Shiite group Hezbollah.
Hezbollah is fighting alongside Assad’s regime, like Iran and Russia.
Israel has expressed growing concern over what it sees as Iran’s attempts to entrench itself militarily in Syria.
It also accuses Iran of seeking to build factories to construct precision-guided missiles in Syria and Lebanon that could be used against Israel.
Beyond that, Netanyahu has warned that Israel will “never let Iran develop nuclear weapons”.
Eisenkot spoke of the “message” of the 2007 strike, while also making reference to a 1981 Israeli raid against a nuclear reactor in Saddam Hussein’s Iraq.
“The message from the 2007 reactor attack was that Israel won’t accept the construction of abilities that could constitute an existential threat to the state of Israel,” he said in the video.
“That’s the message from ’81, that’s the message from 2007 and that’s our future message to our enemies.”
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