The United Nations's second most senior official in Iraq, Jacqueline Badcock, told reporters in Geneva via videoconference: "It is a fatwa (or religious edict) from ISIS, we learnt about it this morning".
"We have no precise numbers," she said on Thursday.
The Islamic State, formerly known as the Islamic State of Iraq and the Levant (ISIS), took over large swathes of the country last month and has begun imposing its extreme Salafist interpretation of Islam.
But several experts have speculated that the fatwa may have been a hoax, and a number of journalists said on Twitter that their contacts in Iraq had not heard of it being issued.
Charles Lister, visiting fellow at the Brookings Doha Center and expert on Iraqi and Syrian extremist groups, said the UN claim appeared to be based on a "quite clearly faked statement" that began circulating online on Wednesday.
"It would certainly be a very big coincidence if the UN source was separate but happened to arise at the same time as this fake statement online," he said.
"FGM just doesn't fit with the Islamic State's image, notwithstanding how brutal an organisation it has proven itself to be."
A spokesman for the UN in Geneva told AFP that "checks" were underway in Iraq, and that until then "nothing had changed."
Badcock earlier said that if you took UN population figures as a guide, around "four million girls and women could be affected" by the alleged fatwa.
Female genital mutilation is unusual in Iraq and is only practised in "certain isolated pockets of the country", she added.
She said only 20 families from the ancient Christian minority now remain in Mosul, the northern Iraq city which ISIS has taken as the capital of its Islamic state. Most have reportedly fled north into Kurdish-controlled territory.
Badcock said some Christians have converted to Islam, while others have opted to stay and pay the jiyza, the tax on non-Muslims the Islamic State has imposed.
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