The ministry said an air strike may have killed Abu Bakr al-Baghdadi and up to 330 other fighters on 28 May.
It said the raid had targeted a meeting of the IS military council in the group’s de-facto capital of Raqqa, in northern Syria.
There have been a number of previous reports of Baghdadi’s death.
Colonel John Dorrian, a spokesman for the US-led coalition fighting IS, said the US could not confirm whether Baghdadi had been killed.
There has been no official comment from Syria’s government.
A statement by Russia’s defence ministry published by the state-funded Sputnik news agency said 30 IS commanders and up to 300 soldiers were at the Raqqa meeting.
“According to information that is checked through various channels, IS leader Ibrahim Abu-Bakr al-Baghdadi, who was killed as a result of the strike, was also present at the meeting,” it added.
Baghdadi’s whereabouts have been unknown for some time, although he was believed to be in Mosul in Iraq before a US-led coalition began an effort to reclaim the city in October 2016.
Reuters reported that he was recently believed to have been “hiding in thousands of square miles of desert” rather than living in either Mosul or Raqqa.
His only public appearance since proclaiming the creation of an IS caliphate was in a video in June 2014, in which he was seen delivering a sermon in Mosul after IS took control of the city.
Since then, the group has lost considerable amounts of territory and has been under pressure from air strikes by Russian-led forces and by the US and its allies.
In March, US Secretary of State Rex Tillerson said that “nearly all” of Baghdadi’s deputies had been killed.
“It is only a matter of time before Baghdadi himself meets this same fate,” he added.
Who is Abu Bakr al-Baghdadi?
Baghdadi – thought to be a nom de guerre rather than his real name – is believed to have been born in Samarra, north of Baghdad, in 1971.
Reports suggest he was a cleric in a mosque in the city around the time of the US-led invasion in 2003.
Some believe he was already a militant jihadist during the rule of Saddam Hussein. Others suggest he was radicalised during the four years he was held at Camp Bucca, a US facility in southern Iraq where many al-Qaeda commanders were detained.
He emerged as the leader of al-Qaeda in Iraq, one of the groups that later became Islamic State of Iraq and the Levant (IS), in 2010.
In October 2011, the US officially designated Baghdadi as “terrorist” and offered a $10m (then £6.4m) reward for information leading to his capture or death.
IS went on to seize Mosul, Iraq’s second-biggest city, in June 2014 before claiming swathes of territory and launching deadly attacks on Western cities, including Paris in November 2015.