"This aggressive conduct by the Zionist entity [pejorative for the State of Israel]… will lead to nothing but an increase in tensions in the region," Syrian news agency SANA cited an official in the ministry as saying.
There was no immediate comment from Tehran.
Earlier, the Israel Defense Forces said that its aircraft had attacked alleged Iranian positions in Syria, firing rockets onto Syrian territory in response to an alleged bombardment of Iranian rockets.
According to IDF spokesman Jonathan Conricus, the Israeli military had informed Russia of the planned airstrikes on Syria.
Tensions between Israel and Iran have been rising recently, as Tel Aviv says Tehran, Damascus' key ally, is trying to increase its military presence in Syria.