The 2013 Kiwi Kids' Good Book Guide lists the book's target age as 13 years and over but Masterton Paper Plus says the book is only suitable for those over 15.
Book manager Sue Reid said, while she usually monitors books when they arrive, the store had initially stocked it as it was a self-publication and had been "flying under the radar".
Mrs Reid said the book had now been removed from shelves.
"While we are saying free speech, and people are free to write what they want, the conflict is that this is a children's book winner. The book is actually aimed at 15-plus and it won in the category 13-plus.
"The content is graphic and people who are pretty liberal have commented on how graphic it is.
"Some of the staff have looked at it, and said 'Oh my goodness'."
Mrs Reid said some Masterton school libraries had chosen not to stock the book, even before it won the award.
Merchandise manager Catherine Raynes said the Paper Plus group left it up to individual stores to make the call.
"We have advised our stores to use the stickers that we sent out with it and advised that the book is for 15-plus and that they need to be aware of that.
"This is not a junior book," she said.
David Hedley of Hedley's Bookshop, in Masterton, said it was not a bookseller's job to be a censor. If a book had been cleared by the censorship authority he was happy to stock it.
"Freedom of expression and publication are an important role for us, as a bookseller."
Mr Hedley was aware the book contains explicit passages and advised discretion but said it was up to the individual to decide whether to buy and read the book.
"It would be quite a disturbing world if there was a limit on what people should buy.
"We shouldn't be the ones deciding that a person can't buy something, unless it's been banned" he said.
The book has been so popular Hedley's has sold out and is awaiting more copies.
Almo's Bookstore owner Steve Lawrence said kids need access to work that is real and relevant to them.
"If you want kids to read, and we do, then they have got to have stuff that is meaningful.
"It can't always be Enid Blyton."
Mr Lawrence said while he has no problem with stocking the book it is up to the individual book store owner.
"Young adults read all sorts of stuff and as long as there is someone around to perhaps have a flick through it and be prepared to talk about things.
"We're not in the business of censoring what is available, people make up their own mind," he said.
