In his will, the late Pope stated that all his personal notes were to be burnt after his death.
But his private secretary, Cardinal Stanislaw Dziwisz, kept them.
He said he did not have the courage to destroy them as  they gave precious insight into the Pope's life and thinking.
The 640-page book, Very Much in God's Hands. Personal Notes 1962-2003, contains Karol Wojtyla's personal reflections on religious subjects from his time as Bishop of Krakow until two years before his death in 2005.
Cardinal Dziwisz recently told reporters he had "no doubt'' about publishing the collection. "These notes are so important, they say so much about the spiritual side, about the person, about the great Pope, that it would have been a crime to destroy them.''
The ideas in the book are briefly sketched, with some written in just two or three sentences, says the BBC's Adam Easton in Warsaw.
The book has its supporters, he continues, but many people in Poland cannot understand why the late Pope's private secretary ignored his wishes.
Adam Szostkiewicz, a prominent religious commentator who opposed the book's publication, says much of it is impenetrable to the average reader.
The cardinal says he spoke to the Pope about which notes should be destroyed and which should be kept.
Cardinal Dziwisz was his closest aide for almost 40 years, first in Poland and then at the Vatican.
After John Paul's death, he was made Archbishop of Krakow in southern Poland.
He has said the proceeds from the book are to fund a memorial museum for the late Pope, who will be declared a saint at the Vatican in April.
A collection of personal notes written by the late Pope John Paul II over four decades is going on sale in controversial circumstances in Poland.