Monsignor Wallace Harris has denied the allegations, "which concern actions that allegedly occurred 20 years ago."
The matter was referred to the Manhattan district attorney's office, which said Monday that the statute of limitations for the complaints had expired.
"If there are any new complaints, we will investigate," spokeswoman Alicia Maxey-Greene said.
The allegations against Harris, 61, were announced during Sunday Mass at the Church of St. Charles Borromeo, where he has been pastor since 1989.
The archdiocese said Harris will not be allowed to practice as a priest pending an investigation by its Advisory Review Board.
Harris led a prayer at Paterson's inauguration in March and served as the event coordinator for part of pope's visit in April, including the Mass at Yankee Stadium.
The church is often referred to as the "cathedral of Harlem" because of its Gothic structure. Pope John Paul II visited the church in 1979.
A message left for Harris at a residence in Harlem went unanswered.
Full statement from the Archdiocese:
An allegation of the sexual abuse of a minor against Reverend Monsignor Wallace Harris, Pastor of Saint Charles Borromeo Parish, has been received by the Archdiocese of New York. In accord with Archdiocesan policy and the Charter for the Protection of Children and Young People of the United States Conference of Catholic Bishops, the matter was immediately investigated by the Archdiocese and then referred to the Office of the District Attorney for Manhattan. The District Attorney's Office conducted its own investigation, in the course of which it received a second allegation, which it subsequently reported to the Archdiocese. Monsignor Harris has therefore been directed to step aside from his position as pastor and is not permitted to function as a priest until such time as the Archdiocesan Advisory Review Board has studied the matter and made its recommendations to the Archdiocese.
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