"The Black Sea fleet's new large diesel and electric submarines, Kolpino and Veliky Novgorod... Have arrived in the Mediterranean," the ministry said in a statement on its website.
It added the stealth submarines, which entered service in 2016 and have a speed of 20 knots under water, are intended to boost the Russian navy's permanent presence in the Mediterranean.
The submarines, both with crews of 50 and built in the northwestern city of Saint Petersburg, are classified by NATO as "Improved Kilo" class.
At Russia's Syrian base of Tartus in the eastern Mediterranean, Russian ships have played a prominent role backing up an aerial bombing campaign in support of leader Bashar al-Assad.
During its military intervention in Syria, Russia has deployed warships, submarines and aircraft carriers to the Mediterranean.
In December last year President Vladimir Putin signed an order to expand the naval base at Tartus and allow Russian warships into Syrian waters.
In January, Moscow and Damascus signed a 49-year deal for Russia to expand and modernise the facility.
According to official figures from last year, some 4,300 Russian military are deployed in Syria.
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