"On September 22 as a result of shelling by the rebels of the Damascus neighbourhood of Mazzeh, one of the shells exploded on the territory of the Russian Embassy in Syria," the ministry said in a statement.
"Three employees received non-life threatening injuries. Right now an investigation of the incident is under way."
The statement did not say whether those hurt were Russian or local employees, but it added that the embassy was looking into additional security measures after the attack.
Russia is a staunch ally of the regime of Syrian President Bashar al-Assad, providing him with diplomatic backing as well as weapons.
Moscow was a key force behind a deal under which Damascus will hand over its chemical weapons stocks for destruction, which headed off a US plan to take military action against the regime.