Here is what really happened - thanks to The Bellarmine Report of Robert Sungenis:
Being on the advisory board of The Kolbe Center for the Study of Creation has its advantages. I have been made privy to one of the most astounding pieces of information I have been privileged to receive since I returned to the Catholic Church 20 years ago. I must also say, however, that although this new information helps solidify my trust in the Holy Spirit’s guidance of the Church, at the same time it makes me realize how corrupt the Vatican apparatus has become. It turns out that the statement attributed to John Paul II about evolution in 1996 (“evolution is more than a hypothesis”) was never stated or written by John Paul II. In fact, John Paul II never even spoke to the Pontifical Academy of Science about the issue. The whole thing was the brainchild of the well-known liberal cleric, Cardinal Angelo Sodano, and his entourage of like-minded liberals. Thank God in heaven that the truth has finally been revealed.
Here are the words of Hugh Owen, director of The Kolbe Center for the Study of Creation, on this very important development:
'The Kolbe Center for the Study of Creation
952 Kelly Rd., Mt. Jackson, VA 22842
Dear Friends of the Kolbe Center,
I would like to share some important information that I recently received from Dr. Dominique Tassot, the publisher of the excellent French journal of the Centre D'Études et Prospectives la Science (CEP). In a recent issue of the CEP journal, a reader submitted the following testimony--from a source which Dr. Tassot considers completely trustworthy. The letter has been translated into English by Mr. Claude Eon:
On October 22, 1996, the scientific community and the popular press gave an account of the message delivered by Blessed Pope John-Paul II to the general meeting of the Pontifical Academy of Sciences gathered in Rome to discuss evolutionary theories. The main part of this message, the one little sentence that made headlines in the papers, is as follows:
Today (...) better knowledge leads us to see in the theory of evolution more than a hypothesis.
This sentence was immediately interpreted as approval by the Holy Father of the principle of biological evolution, in spite of the conflict between this mode of explaining creation and the very foundations of the Catholic religion. However, we now know that John-Paul II never gave this speech. He did not even meet with the members of the Pontifical Academy of Sciences because the planned meeting was canceled.
This is what really happened, according to the unpublished testimony of a priest who was present:
I was a member of this symposium on evolution. Blessed John-Paul II NEVER delivered the speech attributed to him on October 22, 1996. The text, without a signature, was handed over to the members [of the PAS] without any papal audience. After the event, I questioned Father Cottier, now a cardinal. He told me he had himself written a part of the document but that a second writer had intervened, inserting his own additions into the text without showing them to him. (It was precisely the duty of Fr. Cottier, official theologian of the Papal Household, to read all the texts to be signed by the Pope.)
Consequently, the official reviewer could not carry out his mission, He was bypassed. As to John-Paul II, the confidant of his reviewer, he never read or reviewed the text!
Thus we are confronted with a text attributed to Pope John-Paul II and published under his signature in L'Osservatore Romano--but of what real merit? Yet the statement deals with a question of fundamental importance, whether man is only the product of "evolution" or if man, like all that exists on earth, is actually the fruit of a special act of God's Will (betrayed by man's rebellion through Original Sin).
This may also explain why Pope Benedict XVI thought it right to assert the Church's position in his enthronement homily at the inaugural Mass of his pontificate, on Sunday, April 24, 2005, in St Peter's Square:
We are not the accidental and senseless product of evolution. Each of us is the fruit of a God's thought. Each of us is willed, each of us is loved, each of us is necessary.
And that is not all. Here is what the Holy Father added a few months later, on November 9, 2005, after quoting from a commentary on Genesis by the fourth-century bishop St. Basil the Great:
I find that this Father's words are of astonishing relevance when he says: "Some, deceived by their inherent atheism, imagined a universe deprived of direction and order, as if ruled by chance." How many are those "some" today? Deceived by atheism, they believe that it is scientific to think that all is deprived of direction and order, as if ruled by chance. Throughout Scripture, the Lord wakes up man's languid reason and tells us: "In the beginning was the Creative Word." ("Le Cep" N° 60 July 2012, pp. 92-94).
Friends of the Kolbe Center, this letter testifies to the way that the traditional teaching of the Church can easily be subverted by anonymous activists in ecclesiastical offices who misrepresent the mind of the Pope or of the Second Vatican Council to promote ideas that are incompatible with the traditional teaching of the Church. Fidelity to the true teachings of the Church now requires the ability not only to distinguish between the authoritative and non-authoritative statements of the Pope but also to distinguish between the statements merely attributed to the Pope and those that he has actually written or said!
Let us pray that God will deliver the Holy Father from false friends, advisers, and co-workers, and give him the grace to witness boldly to "the faith once delivered to the saints" (Jude 1:3).
Please keep the Kolbe Center in your prayers.
Yours in Christ through the Immaculata,
Hugh Owen' "
 Editor's note: One can gauge the importance of this "little sentence" from the fact that, the very next day, October 24, the conservative daily Il Giornale proclaimed in its headline: "Pope says we may be descended from apes." For La Reppublica, the Pope had "made his peace with Darwin". The following day, Le Monde entitled an anonymous editorial: "Darwin rehabilitated by the Church."
 Editor’s note: One must emphasize the importance of this testimony. The little phrase is indeed, by itself, almost meaningless. But it was interpreted as going beyond the cautious stance assumed by Pius XII in Humani Generis (1950) in which he expressed serious reservations about the evolutionary "hypothesis". "More than a hypothesis" has hardly any intelligible meaning, apart from a theory. Indeed, evolution was already very well-known under the title the "theory" of evolution. Moreover, the letter in question (at least the part written by Fr Cottier) invokes many evolutionist theories, which is a way to relativize them all. A second comment must be made about the disturbing conduct of the Vatican bureaucracy, as the Vatican Secretariat of State itself, which has the duty to write and speak in the Pope's name, indulged in chipping in with a statement [in L'Osservatore Romano] which – what a coincidence –the enemies of the Church were waiting to take advantage of on the very same day. Hmmm....