A mother who left her newborn son in a manger at a New York City church will not face criminal charges for giving him up, a prosecutor said on Wednesday.

A custodian on Monday found the crying infant with his umbilical cord still attached wrapped in towels and placed in the indoor nativity scene at the Holy Child Jesus Church in Queens, New York police said.

The baby's mother was located by police and Queens District Attorney Richard Brown said on Wednesday she would not be prosecuted because she gave up the child in accordance with the state's "Safe Haven" law.

"It appears that the mother, in this case, felt her newborn child would be found safely in the church and chose to place the baby in the manger because it was the warmest place," Brown said in a statement.

Under New York state law, a parent may abandon a newborn anonymously at certain designated safe haven locations, as long as the baby is handed over to an appropriate person.

Father Christopher Ryan Heanue, one of the priests at the church, said he and others placed a clean towel around the baby while waiting for paramedics to show up on Monday.

"The beautiful thing is that this woman found in this church - which is supposed to be a home for those in need -  this home for her child," Heanue said.

"A young couple in our parish would love to adopt this child and keep this gift in our community. It would make a great Christmas miracle," Heanue said.

The healthy baby was taken to a nearby hospital in Queens for evaluation.