The leaders were discussing their exit from the city through the so-called southern corridor, the ministry said.
The US has been informed about the attack, it said.
The strike occurred on the night of May 27 after confirmation of the meeting by a drone.
In Iraq, the US-backed government has been battling to recapture Mosul since October past year after driving the group out of most of the rest of the territory it had seized.
Al-Baghdadi is a nom de guerre for a man identified as Ibrahim Awwad Ibrahim Ali al-Badri al-Samarrai.More news: Amazon buying Whole Foods in bold move into brick and mortar
Since a now infamous 2014 video recording where he declared the establishment of an ISIS "caliphate" from a mosque in Mosul, al-Baghdadi has kept a decidedly low profile aside.
Abu Bakr al-Baghdadi, the leader of ISIS.
CBS News correspondent Holly Williams reports that al-Baghdadi's whereabouts have been a mystery for years - and there have been many rumors of his death before.
According to Putin spokesman Dmitry Peskov, Defense Minister Sergei Shoigu told Friday's meeting that the strike on Raqqa had killed "over 100 militants, among which there were members of the IS leadership, presumably including (IS leader Abu Bakr) al-Baghdadi".More news: Champions Trophy: New Zealand win toss, ask England to bat
A spokesman for the US-led coalition to combat ISIS also released a cautionary statement about al-Baghdadi.
Russian Federation said Friday that it killed ISIS leader Abu Bakr al-Baghdadi and other leaders in a strike in late May, a claim US officials could not confirm. "We have been killing a lot of civilians in and around Raqqa for quite some time now, yet these incidents are rarely admitted by the coalition and there is nearly no interest from worldwide media", said Chris Woods of Airwars this week.
"We can not confirm these reports at this time", said US Army Colonel Ryan Dillon, spokesman for the coalition's Operation Inherent Resolve. With key operations underway against the terror group in Syria and Iraq, spreading such information in this period can leave a positive psychological effect.
The last sign of life from him was in November a year ago, after Iraqi forces supported by the aerial might of the coalition launched their reconquest of Mosul. Al Qaeda leaders later severed relations with him, saying he was insubordinate, killing too many civilians. Since then, IS lost control of territory in Syria and Iraq and has been the constant target of Russian and coalition airstrikes.
There has, however, been no independent confirmation of Baghdadi's death from either USA defense personnel or Iraqi officials. It is likely, Russian and Western military officials believe, to lead to a crumbling of resistance and a rise in the already high number of desertions from the group's ranks.More news: Tesla Inc. (TSLA) Shares Sold by EULAV Asset Management
But soon reports came that he may not have been there.
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