"ISIS continues to defy the will of the world and the feelings of humanity," the ministry said in a statement. "They violated the ancient city of Nimrud and bulldozed its ancient ruins."
The extent of the damage wasn't immediately clear, according to Iraqi state broadcaster Iraqiya TV.
"Our ministry condemns these criminal acts," the statement said. "Letting these lost gangs go without punishment will encourage them to destroy humanity's civilization, the Mesopotamian civilization, inflicting irreversible priceless damages and losses."
Nimrud was a city in the Assyrian kingdom, which flourished between 900 B.C. and 612 B.C. The archaeological site is south of Mosul in northern Iraq.
The razing of Nimrud comes a week after a video showed ISIS militants using sledgehammers
to obliterate stone sculptures and other centuries-old artifacts in the Mosul Museum.
That museum held 173 original pieces of antiquity and was being readied for reopening when ISIS invaded Mosul in June, according to Qais Hussain Rashid, the antiquities ministry's director general of Iraqi museums, who spoke to Iraqiya TV last week.
Nimrud and nearby Nineveh are the sites where two Assyrian kings, Sennacherib (704-681 B.C.) and Ashurnasirpal II (883-859 B.C.), recorded successful military campaigns on the walls of their palaces, according to the World Monuments Fund,
a group dedicated to saving the world's most treasured places.
"Depicted in the reliefs are marauding troops in foreign lands, rendered in a style marked by lively action and attention paid to topographic and ethnographic detail," the fund's website says.
"The palaces of Sennacherib at Nineveh and Ashurnasirpal II at Nimrud are vestiges of the political, cultural and artistic height of the Assyrian Empire. The remains of these palaces, the only Assyrian palaces left preserved and decorated with reliefs, are now protected against vandals and function as site museums where visitors can appreciate ancient wall reliefs in their original setting," the fund said in a website posting before this week's ISIS assault on Nimrud.
King Ashurnasirpal II made Nimrud the royal seat and the military capital of Assyria, Encyclopedia Britannica's website says.
Buildings at Nimrud "have yielded thousands of carved ivories, mostly made in the 9th and 8th centuries B.C., now one of the richest collections of ivory in the world," the encyclopedia says.
ISIS has destroyed other ancient and deeply meaningful sites in Iraq. Officials have said ISIS has blown up shrines such as the tomb of Jonah