Fears have been raised for the future of one of the world's greatest collections of books, after a second flood in 18 months coursed through the National Library of Scotland.

Around 1,000 books were damaged in the main library building in Edinburgh, after the failure of a sprinkler pipe on the top storey caused 5,000 litres of water to run through all 12 floors. The potentially catastrophic incident late on Thursday evening forced 30 library staff to work through the night to clear standing water, and to spend the day beginning the task of drying out the affected volumes.

The threat to a collection of 7 million books and manuscripts which date back to the Middle Ages provoked widespread concern. Like the library flood of September 2007, the incident was blamed on a faulty pipe, which is part of a sprinkler system installed 20 years ago.

Owen Dudley Edwards, an Edinburgh historian who regularly uses the library's reading room, said the two incidents were very worrying and indicative of what he said was the library's Board of Trustees' cosmetic approach to the building. This overlooked the needs of the library's principal users, academics, students and professional writers and researchers, he said.

“I have nothing but admiration for the library staff. The Board of Trustees, however, have undertaken some highly questionable renovations in recent years, which have involved knocking the building to pieces. These days the emphasis is always to make the library more accessible to the general public: it used to be geared to those people who actually use the reading rooms,” Mr Edwards said.

It is not known why the sprinkler pipe failed on Thursday, though the earlier incident was traced to accidental damage caused during renovations to the building.

Experts in rare books and manuscripts expressed relief that none of the most treasured possessions appeared to be damaged. These include thousands of items in the recently acquired John Murray Archive, which contains more than 1,200 hand-written pieces by Lord Byron, and works by Charles Dickens, Charlotte Brontë and Jane Austen, and a manuscript of Charles Darwin's The Origin of Species.

Other works in the library include the Complaint of the Black Knight from 1508, the first printed book in Scotland, and the last letter of Mary Queen of Scots.

Bruce Blacklaw, a spokesman for the National Library of Scotland, confirmed that an investigation into the flood was already under way.

“We are mindful of the fact that this has happened recently. The remit of the investigation will be ensure that any risk to books is minimised now and in the future,” Mr Blacklaw said.

The library was closed while staff dealt with the aftermath of the flood and will reopen on Monday. Damage was reported to be light and the books that were affected were placed in a reading room to dry out with the help of fans and dehumidifiers. It is likely that some volumes will require further conservation work, which will be undertaken over the next few day.

Mr Blacklaw said: “The vast majority of the water has gone out of the building but some has gone into various collection areas.

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