The ministry said Israel had fired “bursts of missiles” from northeast of Lake Tiberias in Israel, targeting the airport and several security checkpoints south of the capital.
Syrian air defenses had shot down some of the missiles, it added.
There was no immediate confirmation if the strike has affected airport operations.
The Israel Defense Forces said that they would not comment on foreign media reports.
Israel’s military has been intensifying missile attacks on Syrian airports, saying that the strikes are meant to target Iranian forces and military assets and prevent Tehran from supplying arms to its allies in Syria, which since 2011 has been locked in a civil war that has killed more than 300,000 civilians.
An Israeli missile strike in the countryside around Damascus killed three Syrian soldiers last month. Air strikes in June put Damascus airport out of service for nearly two weeks.