Pope John Paul, who died in 2005, is being considered for sainthood by the Catholic Church - the ultimate accolade and a tribute to his holiness.
As part of the Vatican's investigation thousands of documents have been collected and examined by officials from the Congregation for the Causes of Saints.
Among them is the testimony of Polish nun Tobiana Sobodka, of the Sacred Heart of Jesus order, who worked for Pope John Paul in his private Vatican apartments and at his summer residence in Castel Gandolfo near Rome.
Sister Sobodka said: 'Several times he (Pope John Paul) would put himself through bodily penance.
'We would hear it - we were in the next room at Castel Gandolfo. You could hear the sound of the blows when he flagellated himself. He did it when he was still capable of moving on his own.'
The flagellation is also confirmed by another bishop who has given testimony Emery Kabongo, who for several years was a secretary for Pope John Paul.
He said: 'He would punish himself and in particular just before he ordained bishops and priests. Before passing on the sacraments he wanted to prepare himself.
'I never actually saw it myself but several people told me about it.'
Sister Sobodka's leaked statements were published in Italian newspaper La Stampa and are part of new book on Pope John Paul II by it's Vatican correspondent.
Self flagellation is sometimes used by devoted Catholics as it reminds them of the whipping endured by Christ at the hands of the Romans before he was crucified.
It is still common in the Philippines and Latin America, some members of strict monastic orders and some members of the lay organization Opus Dei - who feature in the Dan Brown blockbuster The Da Vinci Code.
In the film - which was condemned by the Vatican - murderous Albino monk Silas, who is a member of Opus Dei is seen in a brutal scene whipping his back and drawing blood as he prays on his knees.
Today a Vatican spokesman said: 'The investigation and documentation is still secret and as such we can make no comment on it until the final report is published.
'I know that the nun in question has returned to Poland and she would have spoken with the Congregation as she was with an order that worked in the apartments of Pope John Paul.'
The Congregation for the Causes of Saints has been investigating the case for Pope John Paul since he died and has approved the late pope's 'heroic virtues' and the paperwork has been sent to his German successor.
The late Polish pope's beatification is expected to take place sometime next year, perhaps in April, to coincide with the fifth anniversary of his death or in October to coincide with his election in 1978.
Beatification is the first step in becoming a saint and in order to be granted evidence of a miracle performed by praying to the candidate in question has to be proved and verified by the Vatican.
In the case of Popes the procedure is usually much longer because the Vatican must examine much more material given the mass of responsibility and decisions taken by them as leaders of the Catholic Church.
However, Pope Benedict XVI has put John Paul II's beatification cause on a fast track, waiving a rule requiring a five-year wait before the start of the process.
Following his death in 2005 the vast crowd that gathered in St Peter's Square carried banners bearing the slogan 'Santo Subito' (Saint Immediately).
New reports of miracles attributed to John Paul II's heavenly intervention are said to arrive in Rome every week.
The key one being examined at the moment is the case of French nun Sister Marie-Simon Pierre, 47, said to have been cured from Parkinson's Disease - the same illness suffered by Pope John Paul II - after praying to him.
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