The dust jacket of the book The Irresistible Rise Of Harry Potter gave the impression that it was officially endorsed, lawyers for the author said.
They said its purple colour, typography and use of stars made it look too similar to Rowling's adventures, published by Bloomsbury.
The publishers of the book, Verso, said they had no intention of passing the book off as an officially endorsed product.
The book is an academic text by author Andrew Blake and looks at the books' effects around the world.
"They made it very difficult for us because Bloomsbury used many different colours on the different editions that they printed."
Disclaimer
But they had to pulp the covers and commission a new cover with a disclaimer, a Verso spokesperson said.
The disclaimer read: "Verso is delighted to make it clear that this book is not part of the Harry Potter series.
"Neither the font nor the colour is intended to confuse readers - after all Warner Bros, JK Rowling and Bloomsbury Publishing plc have spent very substantial sums of money marketing and protecting the Harry Potter brand."
"We printed the disclaimer but they weren't happy with that either," the spokesperson said. "They wrote us a rather sniffy letter about it."
It cost the company £5,000 to change the covers.
The old stock has been embargoed until all have the new jackets.
The spokesperson said about 1000 the books had reached bookstores. Bloomsbury had only been aware of them because they had been advertised in The News Statesman.
Arson
They added that it was not the only trouble Verso had with the book.
A case of the books destined to America had been printed with an ISBN number - used on the barcode - that had 666 written on it.
The books were destroyed in a mysterious arson attack at Liverpool docks.
"We're calling it the curse of Harry Potter," the spokesperson said.