It said that Turkish and Israeli military "were informed in a timely manner of the missile launches through communication channels," but it did not mention the United States.
Russia suspended its communication channel with the US about military operations in Syria from Monday after a US jet shot down a Syrian warplane on Sunday, with Moscow accusing Washington of failing to issue a warning.
The defence ministry said in a statement that Russia's Admiral Essen and Admiral Grigorovich warships and the Krasnodar submarine in the eastern Mediterranean fired six Kalibr missiles at command centres and weapons stores in Syria's Hama region.
The ministry added that Russian planes then carried out aerial strikes that "destroyed the remainder of the IS fighters and their facilities."
The most recent such strikes were announced by the ministry on May 31, aimed at targets around Palmyra.
The defence ministry on Friday said that IS this week has been moving forces into Hama province under cover of night and using large buildings there as command points and weapons stores. It said this was part of attempts to move out from Raqa towards Palmyra.