Archbishop Michele Castoro of the Archdiocese of Manfredonia-Vieste-San Giovanni Rotondo, who had recently defended the need for the transfer, presided over the celebration.
On Monday afternoon, a group of 12 friars wheeled the ornate silver vessel containing the body of the saint on a cart in procession from its former resting place to the mosaic-covered crypt of the St. Pio of Pietrelcina Church.
Italian news reports described a scene of thousands of people on hand for the move.
After vespers, the friars accompanied the cart along the route to the new church as the faithful sang hymns.
Once inside the church, the procession stopped for 15 minutes so that the relics could be venerated and so Archbishop Castoro could pause for a moment of prayer.
The archbishop said that "even today, venerating the relics of the Capuchin saint, we are encouraged to imitate his Christian virtues, able to be redirected to a single great path: that of love, love towards God and love towards our neighbor.
"Padre Pio drew (people) to the road of holiness with his own witness, indicating by example the path that led to it: prayer and charity," he said in the address aired by Telenorbo.
He noted that "Pope Benedict XVI reminded us of this during his pastoral visit to San Giovanni Rotondo.”
The Holy Father, who made a pastoral visit to the monastery on June 21, 2009, asked the faithful in his homily from St. Pio Church to live a life of prayer and charity like the great saint.
Following Archbishop Castoro's words, the vessel containing the saint's body was taken to the crypt of the church, which was followed by the celebration of the Eucharist. During Mass, the altar of St. Pio Church was consecrated and the saint's remains were placed inside the church's central pillar.
After the celebration, visitors were free to venerate the relics in their new location, although they were not visible as they were during the expositions in 2008 and 2009, when they were housed in a glass case.
Defending the decision to move Padre Pio's bodily remains, Archbishop Castoro told the online publication St. Francis Patron of Italy earlier this week that while he understands those who were against it, there was also a "need to think of giving an adequate welcome to numerous pilgrims," whom he noted are ever increasing.
The situation has changed in the last 40 years, he added, "and often the crypt proves to be insufficient."
The new location offers a greater capacity for pilgrims and is more comfortably accessed by the disabled, he observed. He added that although people have an understandable affection for the former resting place of the saint, it "doesn't justify the controversy that often is instrumentalized on purpose."
"This is not the teaching of Padre Pio," concluded the archbishop."Being his followers means seeking to imitate him in the docility that he always manifested towards his superiors, also when it caused him suffering."
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