The pupils were there after church leaders thought the area was safe, but IS later launched an attack in what is thought to be an attempt to distract from the Mosul offensive.
The Sunday Express has reported that seven girls were found hiding under beds, under piles of blankets. They had been motionless for seven hours.
Iraq:
Population: 37.5 million, 250,000 Christians
Main Religion: Islam
Government: Parliamentary democracy
World Watch List Rank: 2
Source of Persecution: Islamic extremism
Fr Ammar told the news outlet: "They texted me in the evening, they were terrified - 'We are in danger. Please come for us'. "
The church leader was 60 miles away in the city of Erbil when he received the message.
The Express says he contacted Iraqi and Kurdish forces who planned a rescue operation to get the girls to safety.
Fr Ammar has called the rescue a miracle.
Iraq ranks at number two of countries in the world that persecute Christians, according to Open Doors World Watch List.