Karim al-Nouri, a spokesman for the state-sanctioned force made up mainly of Shiite militias, told state TV they captured the UNESCO world heritage site and were around three kilometres from a nearby town with the same name, without providing further details.
Iraqi forces often claim to have driven IS from areas that are still far from secure, or that quickly fall back into the militants' hands.
Hatra is believed to have been built in the second or third century BC by the Seleucid Empire. IS militants destroyed it along with other major historical sites in and around Mosul after seizing much of northern Iraq in the summer of 2014.
In April 2015, IS released a video showed the extremists smashing sledgehammers into Hatra's walls and firing assault rifles at priceless statues. At one point, the video showed a militant on a ladder using a sledgehammer to bang repeatedly on the back of a carved face until it crashed to the ground and broke into pieces.
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Hatra, located some 110 kilometres southwest of Mosul, flourished during the first and second centuries as a religious and trading centre. It was a large, fortified city during the Parthian Empire and capital of the first Arab kingdom.
The ancient trading centre was surrounded by more than 160 towers. At its heart were a series of temples with a grand temple at the centre - a structure supported by columns that once rose to 100 feet.