The priest, Jorge Laplagne, who presided over two parishes in residential parts of Santiago, allegedly abused a child 13 years ago, the archdiocese said in a brief statement released late Friday.
While the inquiry is underway for a maximum of 60 days Laplagne will not be allowed to carry out any public duties at his San Crescente or Nuestra Senora de Lujan parishes, the statement said.
The archdiocese said it had investigated the priest in 2010, but that the evidence then available was insufficient. It did not describe what evidence might since have surfaced.
In Chile, pope seeks forgiveness for sex abuse scandals
The new case emerged just hours after prominent priest Oscar Munoz, 56, who held senior positions in the Santiago archdiocese, was placed in preventive detention in the city of Rancagua, south of the capital. He is alleged to have raped or sexually abused five children between 2002 and this year.
Some of the victims were reportedly relatives of the cleric.
In January, days before a visit by Pope Francis, Munoz confessed to church authorities that he had sexually abused minors. He was suspended from his priestly duties at that time.
Prosecutors uncovered the abuse when police seized the church's case file during an operation.
In May, the pope accepted the resignations of five Chilean bishops. Four of the five were accused of turning a blind eye to sexual abuse or covering it up.
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