Israeli warplanes struck several targets in Syria early Friday, prompting retaliatory missiles launches, in the most serious incident between the two countries since the Syrian civil war began six years ago.

Syria's military said it had downed an Israeli plane and hit another as they were carrying out pre-dawn strikes near the famed desert city of Palmyra that it recaptured from jihadists this month.

"Our air defence engaged them and shot down one warplane over occupied territory, hit another one, and forced the rest to flee," the army said in a statement carried by state news agency SANA.

The Israeli army denied any planes had been struck and the Syrian government has made similar unfounded claims in the past.

"The safety of Israeli civilians or the Israeli air force aircraft was at no point compromised," army spokesman Peter Lerner told AFP.

The Israeli air force said earlier that it had carried out several strikes on Syria overnight, but that none of the ground-to-air missiles fired by Syrian forces in response had hit Israeli aircraft.

It was an unusual confirmation by the Jewish state of air raids inside Syria.

"Overnight... aircraft targeted several targets in Syria," an Israeli army statement said.

"Several anti-aircraft missiles were launched from Syria following the mission and (army) aerial defence systems intercepted one of the missiles."

None of the missiles fired from Syria hit their targets, the army added.

One missile was intercepted north of Jerusalem by Israel's Arrow air defence system, Israeli media reported.

It would be one of the first times the system has been used.

A Jordanian military source said shrapnel from one missile struck in the north of the kingdom without causing any casualties.

- Air sirens wail -

Both Israeli and foreign media have reported a number of Israeli air strikes inside Syria targeting arms convoys of Lebanese militant group Hezbollah, which fought a devastating 2006 war with Israel and is now fighting alongside the Damascus regime.

The Jewish state does not usually confirm or deny each raid but may have been led to do so this time by the circumstances of the incident.

The missile fire prompted air raid sirens to go off in the Jordan Valley during the night, the Israeli army said.

In April 2016, Prime Minister Benjamin Netanyahu admitted for the first time that Israel had attacked dozens of convoys transporting weapons in Syria destined for Hezbollah.

Israel and Syria are still technically at war, though the border had remained largely quiet for decades until 2011 when the Syrian conflict broke out.

Iranian-backed Hezbollah has been fighting inside Syria in support of President Bashar al-Assad against the rebels.

While there has been periodic stray fire into the Israeli-occupied Golan Heights that has prompted retaliatory strikes, Israel has largely avoided getting sucked into the conflict directly.

Witnesses cited by the press also reported two explosions that could have been caused by the launch of the anti-missile system.

The Arrow 3 interceptor, designed to shoot down ballistic missiles, was handed to air force bases in Israel in January after successful testing by Israel and the United States.

Israel seized most of the Golan Hights from Syria in the Six-Day War of 1967 and annexed it in 1981 in a move never recognised by the international community.

Israel pays close attention to developments in the Syrian conflict for fear that it could be exploited by its arch-rival Iran to install allies close to the armistice line on the Golan and Israel's borders.

In the summer of 2006, Israel and Hezbollah fought a devastating war that killed nearly 1,200 people in Lebanon, most of them civilians, and about 160 Israelis, most of them troops.

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