Capt. 1st Rank Igor Dygalo said the Azov and Yamal landing ships had docked at Tartus to replenish supplies.
He previously said the two warships, which were carrying naval infantry units, would join up with other Russian warships in the Indian Ocean, including the Pyotr Veliky nuclear-powered missile cruiser, for the INDRA-2009 exercise with the Indian Navy in late January.
Russian media recently reported that Russia was planning to set up naval facilities in Yemen (Socotra), Syria (Tartus), Libya (Tripoli), Vietnam (Cam Ranh), among other countries, in the next few years as an alternative to the Sevastopol base in Ukraine's Crimea.
The Soviet-era Navy maintenance site near Tartus is the only Russian foothold in the Mediterranean.
Media reports have suggested the facility could be turned into a base for the country's Black Sea Fleet, which is likely to lose its main base in Sevastopol on the Crimean Peninsula in 2017.
About 50 naval personnel and three floating piers are reportedly deployed at the Tartus site, which can accommodate up to a dozen warships, and Russia is expanding the port and building mooring facilities in nearby Latakia.