There had been previous reports of Baghdadi being killed but they did not turn out to be true.
The air strike was launched after the Russian forces in Syria received intelligence that an Daesh meeting was being planned, the ministry said in a statement posted on its Facebook page on Friday.
“On May 28, after drones were used to confirm the information on the place and time of the meeting of Daesh leaders, between 00:35 and 00:45, Russian air forces launched a strike on the command point where the leaders were located,” the statement said.
“According to the information which is now being checked via various channels, also present at the meeting was Daesh leader Abu Bakr al-Baghdadi, who was eliminated as a result of the strike.”
Al Jazeera’s Rory Challands, reporting from Moscow, said the information was being verified.
“The Russians are certainly not 100 percent confident that the information they believe to be true is actually true,” he said.
“The information is being verified. But if it true, it would be a huge PR coup for the Russians.”
The US-led coalition fighting Daesh said it could not confirm the Russian report.
“We cannot confirm these reports at this time,” said US Army Colonel Ryan Dillon, spokesman for the coalition’s Operation Inherent Resolve.
Al Jazeera’s Stefanie Dekker, reporting from Gaziantep on the Turkey-Syrian border, said “it has been claimed before [that Baghdadi was killed]”.
“It’s [also] been claimed that he’s been injured before, which is why everyone always treats these reports with extreme caution,” she said.
“But it is the first time that we’re hearing this from the Russian defence ministry, and we also had Syrian state media announce this last week.”
The last public video footage of Baghdadi is from 2014 where, dressed in black robe, he is declaring his “caliphate” from the pulpit of Mosul’s medieval Grand al-Nuri mosque.
Born Ibrahim al-Samarrai, Baghdadi, 46, broke away from al-Qaeda in 2013, two years after the capture and killing of the group’s leader, Osama bin Laden.
Rami Abdulrahman, director of the Syrian Observatory for Human Rights (SOHR), cast doubt on the report Baghdadi may have been killed.
He said that according to his information, Baghdadi was based in another part of Syria towards the end of May.
“The information is that as of the end of last month, Baghdadi was in Deir Az Zor, in the area between Deir Az Zor and Iraq, in Syrian territory,” Reuters news agency quoted Abdulrahman as saying.
Questioning what Baghdadi would have been doing in that location, he said: “Is it reasonable that Baghdadi would put himself between a rock and a hard place of the [US-led] coalition and Russia?”
The strike is believed to have killed several other senior leaders of the group, as well as about 30 field commanders and up to 300 of their personal guards, the Russian statement said.