"Undoubtedly, the withdrawal [of the Black Sea Fleet] from the Crimea will affect Russia's security in the south. New bases in the Mediterranean Sea could make up for the departure," Rear Admiral Andrei Baranov said without elaborating.
Russia is set to leave the Sevastopol base when the current lease agreement expires in 2017. The base has been a source of friction between Russia and Ukraine in recent years, as Ukraine's pro-Western President Viktor Yushchenko has sought NATO and EU membership for the country.
Russia has accused Kiev of 'unfriendly' policies toward the Black Sea Fleet base.
Yushchenko has called for the Russian navy's early pullout, tougher deployment requirements and higher fees, demands that have not been backed by his former coalition ally, Prime Minister Yulia Tymoshenko.
Russia-Ukraine tensions heightened after several Black Sea Fleet warships dropped anchor off the Georgian coast during and after the armed conflict with Tbilisi over breakaway South Ossetia last month.
Russia's naval base in the Crimea currently has 50 warships and patrol boats, along with around 80 aircraft, and employs coastal defense troops.
The Soviet-era Navy maintenance site in Syria named Tartus is the only Russian foothold in the Mediterranean.
Russian media reports earlier said the facility could be turned into a base. About 10 Russian warships and three floating piers are reported to be currently deployed there, and Russia is expanding the port and building a pier in nearby El-Latakia. No official confirmation of the reports has been made.
Baranov said Black Sea Fleet and NATO commanders will continue cooperation in the Black Sea and the Mediterranean.
"I do not see why our relations with NATO should end over last month's events," Baranov, said referring to Russia's response to Georgia's offensive to retake South Ossetia in early August.
Western nations criticized Russia's counterattack as excessive and condemned Moscow's subsequent recognition of South Ossetia and Abkhazia as independent states. Russia and NATO have since frozen cooperation.
Russia has blamed Western powers for encouraging Tbilisi's aggression and criticized the alliance for building up forces in the Black Sea and helping Georgia to re-arm in the conflict zone.
Baranov said Russia is meanwhile building up its Black Sea Fleet: "We are learning the lessons of the naval operation to force Georgia to peace"
He said a gunship and a minesweeper have been supplied to the fleet, and new torpedo boats and air defense systems are undergoing tests.