"We offer our condolences to (Villeneuve's) family, whose pain we share", the ministry said in a statement.
However, IS claims that USA aircraft destroyed the mosque, in a statement issued by its news outlet Amaq. "We did not strike in that area".
"The Daesh (Islamic State) terror gangs committed another historical crime by blowing up the al Nouri mosque and its historical al-Hadba minaret", the statement said.
Late Wednesday, the al-Nuri Mosque and iconic leaning minaret in the Old City were destroyed.
CNN's Arwa Damon said Baghdadi's declaration effectively broke down borders between Syria and Iraq, creating a magnet for foreign fighters wanting to join ISIS' cause.
The landmark structure, built in the 12th century, was where IS leader Abu Bakr al-Baghdadi had declared the Islamic caliphate soon after it occupied the Iraqi city in 2014 and the black flag of IS had been flying from the minaret ever since.
The Iraqi armed forces said the militants blew up the mosque as their troops closed in on it on Wednesday.
Erbil- Iraqi forces began storming ISIS-held Old City of Mosul on Sunday, in an assault they hope will be the last in the eight-month-old campaign to seize the militants' stronghold. But a spokesman for the US-lead coalition denied striking the mosque. The event was one of the few times the ISIS leader has been seen in public.
This aerial view taken on June 21, 2017 and provided by Iraq's Joint Operation Command reportedly shows destruction inside Mosul's Nuri mosque compound.
Global organizations estimate that more than 100,000 civilians, of whom half are children, are trapped in extremely risky conditions in the Old City center, the last district still under the militants' control in Mosul.
The coalition is working by, with, and through the government of Iraq to defeat ISIS in Mosul and throughout Iraq. ISIS has has made a habit of destroying antiquities of historical and cultural significance, including parts of the ruins in the ancient Syrian city of Palmyra.
The Syrian army, aided by Russian forces, drove ISIS out of Palmyra a year ago and the liberation was celebrated with an orchestra concert there.
Children have also been forced to take part in violence.
The jihadists have destroyed a string of important heritage sites in Iraq and Syria.
The fall of Shifaa means the Old City in the eastern half of Mosul is now surrounded by US -backed government forces, deployed north, west, south and east, across the river.
The militants are also retreating in Syria, mainly in the face of a US-backed Kurdish-led coalition. The minaret that leaned like Italy's Tower of Pisa stood for more than 840 years. Little did I know it was for the last time.