It happened on Wednesday inside The Church of St. Francis of Assisi around 2:30 p.m.
Police say the suspect went into the church and removed a $3,000 gold-plated metal rose from the memorial.
The memorial commemorates those lost in the 9/11 terrorist attacks, including Friar Mychal Judge, who served as chaplain for the FDNY.
They say the act isn't considered a hate crime, but the the father of the church disagrees.
"We can say this an act of desecration, not just myself, but I got phone calls and people around all day today," said Father Brian Jordan, Pastor at The Church of St. Francis of Assisi.
Jordan says the suspect has been escorted out of the church before, but this time found his way around security directly to the memorial. The suspect broke the rose and walked out the front door before fleeing down 31st Street.
"We're very tolerant, very accepting people's matters," Jordan added. "But when you do a vandalism, destruction of a property and a desecration, then you've you've gone to the limit."
The memorial was at The Church of St. Francis of Assisi was the first one in Manhattan to remember that tragic day.
The gold-plated rose signifies resurrection.
"We lost of our beloved Franciscan friar, Father Michael Judge, and equally important, the loss of our wonderful artwork designer Carole Le Plant, who's a member of the secular Franciscan order," acknowledged Jordan.
Jordan is asking for prayers as the church held a ritual of sanctity for the memorial.
The church is accepting donations to replace the rose with a caveat -- helping out of love and not guilt.
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