The missiles came from the Israeli-occupied Golan Heights and were aimed at the building south of the capital, Damascus, state-run news agency Sana said. There were no casualties.
Sana said Syria’s defence systems intercepted one of the incoming missiles.
Israel carries out raids on Syria mostly overnight and Wednesday’s raid occurred shortly after midnight, Sana said.
The country has staged hundreds of strikes on targets inside the government-controlled parts of Syria over the years but rarely acknowledges or discusses such operations.
However, Israel has acknowledged that it is taking aim at the bases of Iran-allied militias such as Lebanon's powerful Hezbollah group.
It says it is going after arms shipments believed to be bound for the groups. Hezbollah has been fighting on the side of Syrian President Bashar Assad’s forces in the decade-old civil war.
Israel says Iran's presence on its northern frontier is a red line, justifying its strikes on militia-run complexes and weapons caches inside Syria.