"Despite repeated warnings we made to the authorities of the Russian Federation, the military operations by the regime forces continue in Idlib region in violation of the existing memorandums and agreements with the Russian Federation," the ministry said in a statement.
Turkey, which backs rebels fighting Syrian President Bashar al-Assad, blamed "regime forces" for the attack, which it said had killed three civilians and wounded 12.
The Britain-based Syrian Observatory for Human Rights said the attack was carried out by Syrian and Russian air forces, and was aimed at hindering the convoy's advance through Idlib province.
Idlib is supposed to be protected from a massive government offensive by a Turkish-Russian deal struck in September last year.
The Damascus regime denounced the convoy's crossing over from Turkey.
Since late April, Syria and Russia have upped their bombardment of the Idlib region of some three million people, killing more than 860 civilians.