'We used Calibre cruise missiles from the Rostov-on-Don submarine from the Mediterranean Sea,' Shoigu told President Vladimir Putin during an encounter broadcast on state television.
It is believed the cruise missiles can travel as far as 1,500 miles at low altitude to attack enemy strongholds. Shoigu added that Russian strikes launched on Tuesday had been aimed at 'two terrorist strongholds' around Raqqa, the de facto Syrian capital of the ISIS Terrrorist group.
'As a result of the successful launches by the aviation and submarine fleet, all targets were destroyed,' Shoigu said, adding that oil infrastructure, ammunition depots and a mine-making factory had been hit in the strikes.
'The Calibre cruise missile once again showed its effectiveness over long distances.'
Moscow is flexing its military muscle with the latest submarine strikes after having previously fired missiles from warships in the Caspian Sea.
An unnamed source told Interfax news agency earlier Tuesday that a Russian submarine was approaching Syria's Mediterranean coast to launch cruise missiles toward to war-torn country.
President Vladimir Putin said Tuesday that the Caliber cruise missiles launched from the submarine could be equipped with nuclear warheads but said he hoped they would 'never be needed in the fight against terrorism'.
Shoigu said Moscow had warned Israel and the United States - conducting their own bombing campaigns in Syria - that the Russian military would be conducting the submarine strikes.
Shoigu added that Russian military jets had conducted 600 combat sorties and destroyed '300 targets of different kinds' in the past three days.