Lawyers for the police and GCSB sought material from Fisher in the lead up to the trial, that does not yet have a date.
Fisher's book, released on November 18, makes extensive references to interviews with Dotcom about the raids in January 2012.
The Police and GCSB argued that because Dotcom has the legal right to inspect Fisher's documents, they were under Dotcom's control and they should be able to access them, too.
Dotcom's lawyers argued that the book was based on material gathered in the newsmaking process and was therefore an exception under the Privacy Act.
However, Justice Winkelmann found books were not within the definition of news activity by a news medium acknowledged under the Privacy Act.
"...the writing and publication of a book cannot, at least in this instance, be construed as news activity," the ruling said.
News activity was preparing and publishing articles.
"Investigative journalism takes its form in long, detailed articles, which are covered by the Act's definition. Books, however, are not."
Fisher said the ruling could compromise journalism in New Zealand if sources believed their interviews could be obtained through the courts.
"I think the ruling has the potential to undermine the public's confidence in a free press," he said. "The impact of the ruling has a potential chilling effect on anyone who wants to deal with a journalist who is writing a book.
"The only difference between [what the ruling defines as news activity] and what I have produced is that I have stuck a cover on it and put it on a bookshelf.
"That should not give the crown the right to go foraging through my research material based on a loop hole in the law."
His book writing process was no different to his other journalism projects, he said.
"I went about writing the book in the same way I have written every news feature and story I have done in the 25 years I have been a journalist.
"The prospect of that material being used for reasons other than which it was used seems frankly unreal."
Media commentator and journalism academic Jim Tully said books were widely considered as news material and the Privacy Act needed to change if it did not recognise that.
"If that is what the Act says based on Winkelmann's decision, the act needs to be revised," he said. "I share the view that it could have a chilling effect in so far as one of the key principals in investigative journalism is protecting sources and keeping private sources that you have interviewed on that basis.
Mr Tully said there was a long history of New Zealand - and international - journalists publishing books based on their investigations, many of which were indistinguishable to published articles.
The ruling also raised questions about televised journalism, and if news items screened on current affairs shows could be treated differently to a documentary or series, he said.
