Jerusalem (CNN) In the most serious clash between Israeli and Syrian forces since the start of the Syrian conflict six year ago, Israeli aircraft struck several targets in Syria overnight, the Israeli military said Friday.

Israel targeted a military site near the ancient city of Palmyra , the Syrian military said,in what would be one of its deepest airstrikes inside Syrian territory since the civil war began there.

Palmyra, once held by ISIS and retaken by the Syrian government, is strategically important to both the regime and its opponents.

Most of Israel's reported strikes have been around the capital of Damascus, about 60 kilometers (37 miles) from the Israeli-occupied Golan Heights

In response, Syrian forces fired anti-aircraft missiles at the Israeli jets, saying they downed one aircraft and hit another. Israeli vehemently denied the assertions, calling them "absolutely not true."

🔴 Overnight, IAF conducted strikes against several targets in #Syria. Anti-aircraft missiles launched at the aircraft were intercepted. — Peter Lerner (@LTCPeterLerner) March 17, 2017

"At no point was the safety of Israeli civilians or the IAF aircraft compromised," a statement from the Israel Defense Forces said. The statement is unusual in that Israel rarely comments on airstrikes in Syria.

The intercept triggered alarm sirens in the Jordan Valley. Shrapnel from the explosion, which was heard as far south as Jerusalem, landed in western Jordan, the Jordanian military said.

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Syria's latest claims are reminiscent of its statement in September about downing an Israeli aircraft near Quneitra, close to the Golan Heights. Israel seized parts of that region from Syria in the 1967 Six Day War

The Israeli military said then that Syria fired two anti-aircraft missiles at its jets targeting artillery positions, but both missiles missed. They were fired long after Israeli jets left the area, the military added.

Arrow missile defense

One of the missiles overnight was intercepted by Israel's Arrow missile defense system , marking its first operational use. Arrow, Israel's ballistic missile defense system and the long-range version of its Iron Dome , is designed to intercept missiles outside the atmosphere.

The use came more than a year after the first successful Arrow-3 intercept test was carried out in December 2015. At that time, Israeli officials would not say when the missile would become operational.

The Israeli military would not explain why Arrow was used against an anti-aircraft missile, fueling speculation that Israel was either testing the Arrow missile or that its Iron Dome missile defense system wasn't within range of downing the anti-aircraft missile.

Taking aim at weapons smuggling

Israel has long focused on stopping the transfer of weapons from Syria to terror groups.

In December, Israeli Defense Minister Avigdor Liberman told a delegation of European Union envoys that Israel will "prevent the smuggling of sophisticated weapons, military equipment and weapons of mass destruction from Syria to Hezbollah."

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It was another acknowledgement of Israel's ongoing operations in Syria. Last April, Prime Minister Benjamin Netanyahu confirmed that Israel has struck Syria "dozens of times," breaking with the policy of remaining quiet about involvement in its war-torn northern neighbor.

Netanyahu returned last week from Moscow, where he reaffirmed Israel's military coordination with Russia in the skies over Syria. The two countries established the coordination last year to avoid conflicts in Syrian airspace, ostensibly to allow both countries to operate freely. Netanyahu also expressed his concerns about a growing Iranian presence in Syria.

Repeated incursions

Israel has attempted to stay out of Syria's civil war but has reportedly struck the country multiple times in the past, often taking aim at weapons shipments intended for Hezbollah in Lebanon.

As recently as late February, Syrian media reported that Israeli jets hit military positions and weapons convoys near Damascus.

In November 2012, Israel fired warning shots toward Syria after a mortar shell hit an Israeli military post, the first time Israel had fired on Syria across the Golan Heights since the 1973 Yom Kippur War

Israeli jets have been hitting targets in Syria since at least 2013, when US officials told CNN they believed IDF jets had struck nside Syrian territory.

In 2014, the Syrian government and an opposition group both said an IDF strike had hit Damascus' suburbs and airport

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The state-run Syrian Arab News Agency characterized those strikes as "a flagrant attack on Syria, targeting two safe areas in (the) Damascus countryside in Dimas and near Damascus International Airport."

Israeli strikes have also gone after ISIS fighters inside Syria. Late last year, IDF troops operating in the disputed Golan region came under fire from militants of the ISIS affiliate Khalid ibn al-Walid Army, Israeli military spokesman Lt. Col. Peter Lerner said.