The attack was said to have taken place shortly after Donald Trump announced he was quitting the Iranian nuclear deal.
Syrian state news agency SANA reported the sound of explosions, and said Syrian air defences fired at and destroyed two Israeli missiles.
A commander in the regional alliance supporting Bashar al-Assad, the Syrian dictator, told Reuters that Israel’s air force had struck an army base without causing casualties.
There was no immediate comment from Israel, which almost never confirms or denies airstrikes in Syria.
An April 9 strike killed seven Iranian military personnel at a Syrian airbase. Iran blamed Israel and vowed to retaliate. Israel’s military said it was seeing signs of “irregular activity of Iranian forces in Syria” and ordered Israeli civilians in the Golan Heights to ready their bomb shelters.
“Defence systems have been deployed and Israel Defense Forces troops are on high alert for an attack,” a military spokesman said.
“The IDF is prepared for various scenarios and warns that any aggression against Israel will be met with a severe response.”
Some reserve troops from military intelligence, air defence, and the home front units were called up, according to Israeli media, but the military stopped of a full scale mobilisation of reserves.
The Israeli education ministry also cancelled all school trips to the Golan Heights scheduled for Wednesday.
“Israel fully supports President Trump’s bold decision today to reject the disastrous nuclear deal,” Mr Netanyahu said in a speech moments after Mr Trump’s address.
The Israeli leader has consistently warned that the deal would pave the way for Iran to build an arsenal of nuclear weapons and called the agreement a “recipe for disaster”.