The ministry did not say when the switch at the base at Tartus took place or how many personnel were deployed there.
The minor facility is Russia's only naval outpost outside the former Soviet Union. It consists of several barracks and depots used to service Russian navy ships in the Mediterranean.
The ministry statement said that Tartus has continued to service the Russian navy ships.
"They are continuing to work in a regular mode, and there is no talk about their evacuation from Tartus," the statement said. "Tartus remains the official base and repair facility for the Russian ships in the Mediterranean and is continuing to fulfill its mission."
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Moscow, however, also has an unknown number of military advisers in Syria who help its military operate and maintain Soviet- and Russian-built weapons that make up the core of its arsenals.
Russia has been the main ally of Syrian President Bashar Assad, shielding his regime from the UN Security Council's sanctions and continuing to provide it with weapons despite the two-year civil war that has killed more than 93,000 Syrians, according to the UN estimates.
In Washington, US State Department spokesman Patrick Ventrell refused conjecture about the Russian move, but pointed at the "deteriorating security situation."
"I just can't speculate if that's their reasoning," he added.
Russia announced earlier this month that it will keep a fleet of about dozen navy ships in the Mediterranean, a move seen as an attempt to project power and protect its interests in the region.