Updated at 12:29 pm today
Some independent stores have followed suit, including Unity Books which has stores in Auckland and Wellington.
Auckland owner Jo McColl says she had ordered three copies of the book but will now probably bin them.
Ms McColl says she has been disturbed by coverage of this week's inquest into the twins' deaths and thinks no one should profit from the situation.
The refusal to stock the book comes after a 38,000 members on a Facebook page called for a boycott.
Former publisher Graham Beattie says he is surprised by the retailers' reaction.
Mr Beattie says giving into pressure groups sets a dangerous precedent, especially when it comes to other books about contentious subjects.
New Zealand Booksellers Association chief executive Lincoln Gould says retailers make choices all the time about what books to stock and they have the right to choose not to sell one.
But he worries that some people who have not even read the book are threatening to boycott any store that sells it.
An inquest into the unexplained deaths of babies Cru and Chris Kahui is expected to finish in Auckland on Thursday.