On June 24, Israel's military said it launched a Patriot missile at an incoming unmanned aerial vehicle, which turned away unharmed.
The drone had come from Syria, traveled into Jordan, and then crossed over into Israel.
The group of more than 40 mothers and children that crossed over in the pre-dawn hours of Wednesday were among the 3,000 Syrians who Israel says have received separate treatment in what it calls "Operation Doctor's Appointment".
There was no immediate comment from the Israeli military.
According to state-run SANA, "Syrian air forces intercepted an Israeli aggression and downed a number of missiles which were targeting T-4 airport in Homs". "The IDF will not allow any violation of Israeli airspace and will act against any attempt to hurt its civilians".
He added that military officials believe the drone was Syrian and that it could have been on an intelligence collecting mission, but it was not yet clear if it purposely entered Israel or strayed from its path.More news: Warrior Nadal downs Del Potro in thriller to reach semi-finals
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Russian Federation was already working to distance Iranian forces from areas of Syria near the Israeli-occupied Golan Heights and had proposed that they be kept 80 km (50 miles) away but this fell short of Israel's demand for a full exit, the official said.
Israel held out the prospect on Tuesday of eventual contacts with Syria under President Bashar al-Assad, in a nod to his regime-consolidating advances in a seven-year-old civil war that Israeli officials had initially predicted would topple him. "Obviously, our focus is on Syria and Iran".
Responding to a reporter's question if Israel would establish some kind of relations with Syria, Lieberman responded: "Our assessment is that we are far from that, but we do not rule out anything".
Iran is backing Syrian President Bashar al-Assad in the war, as is Russian Federation.
Russian Federation also has maintained warm ties with Israel and demonstrated a readiness to take its security interests into account.
Israel, which captured the Golan Heights from Syria in the 1967 Middle East war, has largely stayed out of the current conflict.