"For the first time in our naval history, the aircraft carrier Admiral Kuznetsov started taking part in combat," Shoigu said at a meeting with President Vladimir Putin in the Black Sea city of Sochi, according to televised footage.
"Today from this carrier, our Sukhoi-33 (bombers) began their operations", he said.
Russia has been carrying out a bombing campaign in Syria for the past year in support of its ally President Bashar al-Assad and deployed a naval contingent to back up its operation.
The Admiral Kuznetsov, Russia's sole aircraft carrier, arrived in the eastern Mediterranean off the Syrian coast as part of a flotilla of ships sent to reinforce Russia's military in the area.
The biggest naval deployment of recent years saw the flotilla sail from Russia's Arctic waters down through the North Sea and along the Channel.
This prompted NATO chief Jens Stoltenberg to warn the ships could be used to take part in air strikes in Syria and "increase human and civilian suffering."
During initial flights from Admiral Kuznetsov aircraft carrier, a Russian MiG crashed into the sea while attempting to land, the defence ministry said Monday.
The pilot ejected and was rescued unhurt, it said.
Shoigu said the "major operation" began at 0730 GMT Tuesday aiming to inflict heavy damage on "the Islamic State group and the Al-Nusra Front's positions in Idlib and Homs provinces."
The operations targeted stores of ammunition and factories producing chemical warfare agents. "They will continue," Shoigu said.
The naval fleet is protected by S-400 and S-300 air defence systems that "cover the sea area practically to Cyprus" as well as by Bastion missile complexes on shore, the defence chief said.
"Today we are able to hit both sea and land targets across almost 350 kilometres (218 miles) of sea and almost 450 kilometres of land," Shoigu said.