Protesting campaigners had tied the tiny shoes to the railings outside St Mary's Pro-Cathedral in Dublin in advance of Easter services on Sunday.
Frank Robinson, who bought the shoes for about €4,200, became concerned when they mysteriously disappeared on Sunday afternoon.
However, it emerged yesterday that the shoes had been stored in the parish office of the pro-cathedral after staff took them down from the railings.
A spokesperson for the Archdiocese of Dublin said the shoes had been removed after the events on Sunday. They were handed back.
Mr Robinson said he hoped the shoes, bound together with a piece of black ribbon, would become a global symbol for the generations of children who fell victim to institutional child abuse.
"I want to spread this right around the world," he said of his 'Baby Shoes Remember' project.
There were angry scenes outside the pro-cathedral at the weekend when Archbishop Diarmuid Martin was confronted by abuse survivors.
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