Since Syria's civil war erupted in 2011, Israel has carried out hundreds of strikes in the country, mainly targeting army positions and Iran-backed fighters, including Lebanon's Hezbollah.
The strikes have increased in recent days, including on areas near the border with Lebanon.
"At approximately 20:05 (17:05 GMT) the Israeli enemy launched an air aggression coming from the direction of north Lebanon, which targeted military sites in the central region, causing material losses," the ministry said in a statement.
Earlier, state media said Syrian air defences were intercepting "hostile targets" in central Syria, a phrase commonly used to refer to Israeli strikes on the war-torn country.
"Israeli strikes" targeted a "weapons depot south of Homs and a rockets depot in the eastern Hama countryside," Rami Abdel Rahman, head of the Syrian Observatory for Human Rights War Monitor, told AFP.
Rahman, whose Observatory is based in Britain, added that the sites belonged to the Syrian army.
Earlier on Sunday, an Israeli strike in Syria targeted trucks transporting aid for Lebanese people, wounding three aid workers, the Observatory said.
On Friday, Lebanon said an Israeli air strike on the Syrian border cut off the main international road linking the two countries.
Israeli authorities rarely comment on individual strikes in Syria, but have repeatedly said they will not allow arch-enemy Iran to expand its presence there.
Tens of thousands of people have crossed into Syria over the past week, fleeing heavy Israeli air strikes on Lebanon.
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