Earlier, the Israeli military said Iranian forces in neighbouring Syria fired rockets at their positions in the occupied Golan Heights.
"This was an operation we prepared for, and were not surprised by", said Lt. Col. Jonathan Conricus, a spokesman for the Israeli military.
The attack took place at around 12.10 a.m.
"We have retaliated, but I have no further details about this", he said, according to Reuters.
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The tensions worry Russian Federation, which wants to stabilise Syria.
The reports of an Israeli attack in Kisweh late on Tuesday emerged after US President Donald Trump announced he was pulling out of the Iranian nuclear deal.
Dozens of missiles were shot down by anti-aircraft systems in Syrian airspace.
Israeli strikes targeted military bases, air defense units and radar installations, Syria's state news agency SANA said.
Just before midnight Wednesday, Syria state news agency reported that rockets suspected to be coming from Israel hit southern Syria's Quneitra province.
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Israeli Prime Minister Benjamin Netanyahu said on Wednesday evening that Israel has the "obligation and right" to defend itself against Iranian aggression from the Syrian territory. Hours later, state-run Al-Ikhbariya TV broadcast a live feed of Syrian air defenses firing into the sky above the capital, and loud explosions and air defense firing were heard through the night.
A man inside a bomb shelter in the northern Israeli city of Safed, May 8, 2018. There was no official confirmation.
Israel has repeatedly clashed with Hezbollah, a Shiite militia based in Lebanon and sponsored by Iran.
"It's hard to believe, but 73 years after the Holocaust, in our Middle East there is a country Iran that openly calls for the destruction of the state of Israel", he said in translated comments. The occupied Golan Heights has been on high alert since Donald Trump confirmed he was pulling the United States out of the Iran nuclear deal.
He said they targeted intelligence, logistics, storage and vehicles as well as the origin of the rockets.
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Members of the Iranian Revolutionary Guards Corps' Quds Force, fighting in Syria in support of Syrian dictator and longtime Iranian ally Bashar Assad, were responsible for the strikes, IDF Spokesperson Ronen Manelis told Israeli news outlet Haaretz.
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