The Kurdish regional government says schools will open as planned next Wednesday but, on top of the huge challenge of educating those who have been displaced, there are major concerns about where those now living in schools will be moved.
"It is a major disaster for children," said Brenda Haiplik, an education expert from the UN children's agency, UNICEF.
"Education is life-saving. After a child has been to hell and back, education gives him or her an opportunity to go forward. Without that, the future is dim."
Swathes of Iraq have been seized by militants since the beginning of the year, especially in a major jihadist-led offensive launched in June, causing widespread displacement of people desperate to escape the unrest.
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With unsanitary camps scattered across the north overflowing with Iraqis who fled their homes, thousands of families have sought refuge in schools.
In Dohuk, the worst-affected Kurdish province, more than 600 schools are now home to displaced families.
"We are facing an education emergency" that affects the displaced, the more than 200,000 Syrian refugees in the Kurdistan region and local children alike, Haiplik told AFP.
"And as soon as housing is provided (for displaced families), we are ready to cover their educational needs," Sadiq told AFP.
But he admitted the authorities are struggling to find shelter for the displaced.
"The Kurdistan government doesn't have the infrastructure to give shelter to the displaced. And assistance from the international community is very slow," he said.
With the deadline for the start of the academic year looming, schools in the region's capital Arbil were still home to thousands of displaced people, with up to four families sharing a single classroom.