It said troops were "on high alert for an attack" in the area, which is Syrian territory under Israeli control.
Meanwhile Syria said an Israeli air strike had targeted an area south of Damascus.
It came as President Trump said the US would quit the Iran nuclear deal.
Israeli Prime Minister Benjamin Netanyahu said he "fully supports" Mr Trump's withdrawal, saying the deal had "increased Iranian aggression".
"For months now, Iran has been transferring lethal weaponry to its forces in Syria, with the purpose of striking at Israel... We will respond mightily to any attack on our territory," he said
In a statement, the Israeli military said defence systems had been deployed in the Golan Heights.
Israeli media said it was the first time there had been an order to prepare shelters in the occupied area since the Syrian civil war began, Reuters reported.
"Any aggression against Israel will be met with a severe response," spokesman Jonathan Conricus said.
Strikes in Syria
Meanwhile, Syria's state news agency Sana said Syrian air defences had destroyed two Israeli missiles in the Kiswah area.
The strike had targeted a Syrian army position but did not cause casualties, a pro-Assad commander told Reuters.
Iran has vowed to avenge recent air strikes on its military facilities in Syria that were attributed to Israel.
Israel has neither confirmed nor denied carrying out the strikes, but it has said it will stop what it considers Iran's military "entrenchment" in Syria.
Israel is also thought to have bombed arms shipments intended for Lebanon's Hezbollah movement - supported by Iran - several times since the Syrian conflict began.
Iran has backed President Assad throughout Syria's seven-year civil war, deploying hundreds of military advisers and thousands of militiamen to the country.
Israel seized the Golan Heights from Syria in the closing stages of the 1967 Six-Day War and unilaterally annexed it in 1981. The move is not recognised internationally.
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