"According to the information which is now being checked via various channels, also present at the meeting was Islamic State leader Abu Bakr al-Baghdadi, who was eliminated as a result of the strike", the ministry said.
The airstrike was carried out on May 28 against a command post, where the IS group's leaders were meeting to discuss the routes for the terrorists' exit from Raqqa through the "southern corridor", the ministry said in a statement.
"The preemptive airstrikes, which the Russian Aerospace Forces carried out on the sites of ISIL facilities on June 6 and June 8, killed ISIL field commanders Abu Omar al-Baljiki and Abu Yassin al-Masri".
There had been numerous reports in the past of al-Baghdadi being killed, but they did not turn out to be true.
The Russian air force launched an air strike between 00:35 and 00:45 local time (21:35 and 21:45 GMT 27 May), after notifying the USA military in advance.
ISIS fighters are close to defeat in the twin capitals of the group's territory, Mosul in Iraq and Raqqa in Syria.
In Iraq, the USA -backed government has been battling to recapture Mosul since October previous year after driving the group out of most of the rest of the territory it had seized.
If true, then it would mark a major military success for Russian Federation, which has been conducting a military campaign in support of Syrian President Bashar al-Assad since September 2015.
The Russian military initially sent drones to monitor the area and then dispatched a group of Su-34 bombers and Su-35 fighter jets to hit the ISIS gathering.
Baghdadi has been rumoured wounded or killed a number of times in the past.
To support the Kremlin's narrative that it was conducting pinpoint strikes against ISIS, the Russian Ministry of Defense released YouTube videos of several airstrikes purportedly against the terrorist group.
Al-Baghdadi is a nom de guerre for a man identified as Ibrahim Awwad Ibrahim Ali al-Badri al-Samarrai. Other reports also spoke about the killing of another leading official from the Kurdish People's Protection Units in an explosion that targeted his convoy in the town of Ain Issa, in the countryside of northern Raqqa.