The news agency did not give further details and it was unclear who was behind the attack, which Syrian state television branded as an "aggression".
Syrian news agency SANA stated that "Syrian air defense shot down missiles which violated airspace over Homs".
Syrian state media is widely believed to exaggerate their claims of shooting down incoming missiles.
Following reports of an Israeli strike, an Israeli military spokesman said: "I'm not aware of such an incident". Check back for updates.
The Pentagon has denied initiating strikes or conducting any other military activity in Homs province.More news: Kendrick Lamar Makes History With Pulitzer Prize Win for DAMN
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Hezbollah's AlManar TV reported that six missiles targeted Shayrat and three were aimed at Dumair military airport outside Homs on Monday.
On April 14, 2018, the United States, the United Kingdom and France launched cruise missiles at Syria's military and civilian infrastructure. The US Department of Defense spokesman, meanwhile, told Sky News Arabia that there are "a lot of players" in the region who could have carried out the Tuesday morning attack in Syria.
Also a number of local reporters have said there are "Israeli warplanes" flying at high-altitude carrying out the attack after crossing the borders through Lebanon.
Before the USA -led attack, Israeli warplanes had fired missiles on the T-4 airbase in the eastern countryside of Homs on April 9, killing 14 soldiers, including Iranian fighters.