"The Israeli enemy launched an air attack from the direction of Lebanon, targeting a central site and a residential building in Baniyas city in the coastal region, killing a girl and wounding 10 civilians," a ministry statement said.
The Syrian Observatory for Human Rights war monitor also reported the girl's death and put the civilian wounded toll at 20.
The Britain-based Observatory also said the Israeli strike on central Syria killed three Syrian fighters working with Lebanon's Iran-backed Hezbollah group and two other non-Syrian fighters working for the same movement.
Earlier on Wednesday, state media said air defences intercepted Israeli "targets" over central Syria.
"Syrian air defence intercepts enemy targets in the skies of the city of Homs," the official SANA news agency reported.
The Observatory said the Israeli strikes targeted "at least one military site... in the eastern countryside of Homs, causing plumes of smoke to rise".
On Saturday, an Israeli drone strike in central Syria, near the border with Lebanon, killed two Hezbollah fighters, the Observatory had said.
Israel rarely comments on individual strikes in Syria but has repeatedly said it will not allow its arch-enemy Iran to expand its presence there.
Israel has carried out hundreds of strikes in Syria since the outbreak of the civil war in its northern neighbour, mainly targeting army positions and Iran-backed fighters including from Hezbollah.
The strikes have increased since Israel's war with Hamas in the Gaza Strip began on October 7, when the Iran-backed Palestinian militant group launched an unprecedented attack against Israel.
Syria's war has killed more than half a million people and displaced millions more since it erupted in 2011 after Damascus cracked down on anti-government protests.
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