The Iraqi city of Mosul was once a majority-Christian city, but is now an Islamic State (IS) stronghold, where militants have repurposed deserted church buildings as prisons.
Fides news agency reports that detainees were held at the ancient Chaldean Church of the Immaculate Conception in the eastern part of the city, having been blindfolded and handcuffed.
St George's monastery has also allegedly been used as a female detention centre.
Reports circulated last week that the nearby convent of the Chaldean Sisters of the Sacred Heart had been bombed by IS militants.
Several other Christian churches, Yazidi shrines and Shiite mosques have also been demolished by the group that has declared a caliphate in large parts of Iraq and Syria.
Almost all of Mosul's Christian inhabitants were driven out in June, given the choice of conversion to Islam or death.