It also reported that the missiles were shot down by the country's air defenses.
Six missiles targeted the Shayrat airbase in the central province of Homs and the Syrian air defenses intercepted majority, said the report, adding that three other missiles targeted the Dumair airbase in the Dumair area in the eastern Qalamoun region north of Damascus and were all intercepted before reaching their targets.
Meanwhile, the state news agency SANA reported the overnight attack in Homs, spelling no further details but added that the source of the missile strike is not yet known amid speculations that Israel is more likely to be behind the attack after the Pentagon denied carrying out operations on the aforementioned airbases.
Observatory chief Rami Abdel Rahman said missiles did not hit any of the air bases.
The tripartite attack was in ostensible retaliation for an alleged chemical weapons attack by the Assad regime on the Syrian city of Douma, which is said to have killed scores of civilians.
In Washington, Pentagon spokeswoman Heather Babb said: "There are no USA or coalition operations in that area".
Shayrat air base was targeted by US Tomahawk missiles in April a year ago in a strike ordered by President Donald Trump in retaliation for a suspected chemical attack on the rebel-held town of Khan Sheikhun in Idlib.