Thousands of rare books and manuscripts in Iraq's national library and archive, one of the country's most important cultural institutions, are in peril after the occupation of the building by Iraqi security forces, the library's director said yesterday.

Saad Eskander, a respected Kurdish historian who has run the library since 2003, told the Guardian that up to 20 Iraqi troops had seized the building at gunpoint yesterday, threatening staff and guards.

"They have turned our national archive into a military target," he said. "Tomorrow or the day after, the extremists will attack the Iraqi forces there."

He said the soldiers, who said they had occupied the building to defend Shia worshippers heading to the shrine of Khadimiya, about 15 miles away, had positioned themselves on the roof of the library. They had already started to dismantle the main gate, and had smashed doors and windows inside the main building, he said.

He fears soldiers may start looting the building "or even set fire to it".

Like Iraq's national museum, the library and archive was badly damaged in the chaos that gripped Baghdad following the collapse of Saddam's regime. Large parts were gutted by arsonists, and pillaged by looters. More seriously, the library estimated it lost 25% of its collections, including many rare books, while the archive lost 60% of its collections, including irreplaceable records from the Ottoman era. Since then, Mr Eskander and his team have rebuilt the library and archive, winning respect around the world. He has also kept a blog detailing his daily travails and the plight of his city. It can be read on the British Library website.