Leaked library borrowing cards from half a century ago revealed the teenage Murakami -- nowadays a perennial contender for the Nobel literature prize -- checked out several titles by French writer Joseph Kessel.
But the Japan Library Association on Monday lashed out at what it said was an invasion of the publicity-shy writer's privacy.
"Disclosing the records of what books were read by a user, without the individual's consent, violates the person's privacy," said an association report.
The Kobe Shimbun, which published the report, stood by its decision today, saying that what the 66-year-old Murakami read decades ago is in the public interest.
"Mr Murakami is a person whose work and how he developed his literature are a subject for scholarly study," Hideaki Ono, Kobe Shimbun's assistant managing editor, told AFP.
"He is known to have profound knowledge of British and American literature. But (the cards) showed he also explored French literature in his younger days. We believed these facts are of high public interest."
The controversy began when a volunteer at Kobe High School, the author's alma mater, found three books with cards still attached showing a student named "Haruki Murakami" was among those who had borrowed them.
The volumes were discovered among old library books about to be discarded by the school, the report by the library association said.
The volunteer then contacted the newspaper regarding the find about Murakami, who went on to become the author of widely read works including "Norwegian Wood," "The Elephant Vanishes," and "The Wind-Up Bird Chronicle".
The school, meanwhile, has apologised for the information being divulged, the library association report said.
Murakami, whose novels centre on the absurdity of modern life, has not publicly commented on the furore.
Kessel was a well-known literary figure in France whose books continue to be read.
His works include "The Lion" and "Belle De Jour", which inspired the film of the same name, starring Catherine Deneuve.
Follow NDTV for latest election results and live coverage of assembly elections 2019 in Maharashtra and Haryana.
Subscribe to our YouTube channel, like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.