Titled "I'm Very Much in God's Hands", the 640-page book delves into often obscure theological notions penned by Karol Wojtyla between 1962 and 2003, before and during his papacy.
An enigmatic passage from March 1981 mentions sinful Catholic clergy, but stops short of revealing whether the pontiff had in mind the wave of paedophile offences involving priests.
"Don't the sins of bishops and priests burden Christ with a greater cross, than those of others?" says one entry by the late pontiff, who will be canonised as a saint in April just nine years after his death.
But Dziwisz, who is now cardinal, said he felt it would be "a crime" to destroy them, sparking criticism and shock that he would ignore the pope's last wishes.
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"The pope left a part of his soul here, his experience of God, his meditations and devotion, and it's this that makes this publication so valuable," Dziwisz told reporters in Poland in the run-up to book release.
"These are such important ideas, focused on spirituality and humanity, from a great pope that it would be a crime to destroy this," added Dziwisz.
"It is a violation of his last will and testament, and in European culture it is always binding," said Father Tadeusz Isakowicz-Zalewskihe in a comment posted on the Internet.
"Shame on Cardinal Dziwisz for publishing the Pope's personal notes against his wishes," said Breeanne Howe in a tweet today.
Dziwisz served as Wojtyla's chief aide for nearly 40 years, first during his years as a cardinal in Krakow and at the Vatican after his historic 1978 election as the first Polish pope.