The Russian strike started at 2135 GMT on May 27 (12:35 am on May 28 local time) following confirmation of the meeting by a drone.
The ministry said an air strike may have killed Abu Bakr al-Baghdadi and up to 330 other fighters on 28 May.
There had been previous reports of Baghdadi being killed but they did not turn out to be true.
"According to the information that is being verified through various channels, IS leader Abu Bakr al-Baghdadi also attended the meeting and was killed in the air strike", the ministry said.
The jets struck when the IS leaders had gathered to plan a pullout from Raqqa.
Russian forces support the Syrian government which is fighting against Islamic State mainly from the west, while a USA -led coalition supports Iraqi government forces fighting against Islamic State from the east.More news: UK authorities charge Welsh man in mosque attack with murder
Reports of al-Baghdadi's death regularly surface, but the statement Friday was the first time Russian Federation acknowledged that it may have killed him.
Baghdadi's location has been unknown for sometime, although he was believed to have been in Iraq in October 2016, the BBC reported.
Russia's statement comes as the USA -led coalition tries to remove Islamic State from its self-declared capital of Raqqa, a city the jihadist group has brutalized since 2013, and used as a base to plot terrorist attacks in Europe.
This is the first time, however, that Russian Federation has said it may have killed the IS leader. This claim has not been verified as of yet, but it was reported that it occurred at the end of May during one of the air strikes on the city of Raqqa in Syria.
A week later, Baghdadi surfaced with an audio tape that called for "volcanoes of jihad" around the world.
Incidentally in June past year, reports had also claimed that the ISIS leader was killed in an air raid by the US-led coalition. Reports later said he had made a slow recovery.