The Israeli military has said it attacked nearly all of Iran's military installations in neighbouring Syria in response to an Iranian rocket barrage on Israeli positions in the occupied Golan Heights.

It is the most serious military confrontation between the two bitter enemies to date.

Israel said the targets of the strikes, its largest in Syria since the 1973 war, included weapons storage, logistics sites and intelligence centres used by elite Iranian forces in Syria.

It also said it destroyed several Syrian air defence systems after coming under heavy fire and that none of its warplanes were hit.

Iranian media described the attacks as "unprecedented", but there was no official Iranian comment on Israel's claims.

Syria's military said the air strikes killed three people, wounded two and destroyed a radar station, an ammunition warehouse, and damaged a number of air defence units.

Brigadier General Ali Mayhoub, who read the statement on television, said Syrian air defence systems had intercepted "the large part" of the incoming Israeli strikes.

Israel has acknowledged carrying out more than 100 air strikes in neighbouring Syria since the civil war erupted in 2011, most believed to be aimed at suspected Iranian weapons shipments bound for the Hezbollah militant group.

But in the past few weeks, Israel has shifted to a more direct and public confrontation with Iran, striking at Iranian bases, weapons depots and rocket launchers across Syria, and killing Iranian troops.

Israel accuses Tehran of seeking to establish a foothold on its doorstep. Iran has vowed to retaliate.

Reflecting the scope of the overnight attacks, Russia's military said 28 Israeli jets were involved, striking at several Iranian and government sites in Syria with 70 missiles. It said half of the missiles were shot down.

Defence minister Avigdor Lieberman said Israel would respond fiercely to any further Iranian actions.

"We will not let Iran turn Syria into a forward base against Israel," he said.

"We, of course, struck almost all the Iranian infrastructure in Syria, and they need to remember this arrogance of theirs. If we get rain, they'll get a flood. I hope that we ended this chapter and that everyone understood."

The Britain-based Syrian Observatory for Human Rights, which closely monitors the civil war through sources inside Syria, said the overnight Israeli attacks struck several military posts for Syrian troops and Iranian-backed militias near the capital, Damascus, in central Syria and in southern Syria.

The observatory said the attacks killed 23 fighters, including five Syrian soldiers. It said it was not immediately clear if Iranians were among those killed.

Damascus shook with sounds of explosions just before dawn, and firing by Syrian air defences over the city was heard for more than five hours.

Israel said early on Thursday that Iran's Quds Force fired 20 rockets at Israeli front-line military positions in the Golan Heights.

Israel captured the Golan Heights in the 1967 war, annexing it in 1981 in a move not recognised internationally.

In 1974, Israel and Syria reached a ceasefire and a disengagement deal that froze the conflict lines with the plateau in Israeli hands.

Lt Col Jonathan Conricus, a military spokesman, said four of the rockets were intercepted, while the others fell short of their targets. The incoming attack set off air raid sirens in the Golan.

He said Israel was not looking to escalate the situation but that troops will continue to be on "very high alert".

"Should there be another Iranian attack, we will be prepared for it," he said.

It is believed to be the first time in decades that such firepower from Syria has been directed at Israeli forces in the Golan Heights.

Iran's ability to hit back further could be limited. Its resources in Syria pale in comparison to the high-tech Israeli military and it could also be wary of military entanglement at a time when it is trying to salvage the international nuclear deal.

Iran has sent thousands of troops to back Assad, and Israel fears that as the fighting nears an end, Iran and tens of thousands of Shiite militiamen will turn their focus to Israel.