"We have apologized to the victim and now I am repeating it publicly, and we also ask for forgiveness from the community for the scandal that this has caused," San Salvador Archbishop José Luis Escobar Alas said in a news conference after celebrating Mass.
"At the same time we pray for the victim and also for the priest," he said.
The victim was received by the Archdiocese's Commission on Childhood Protection, which according to Escobar, "found merit in their accusation and suggested that the proper canonical process be initiated."
The priest, identified as Leopoldo Sosa Tolentino, was suspended, the archbishop said.
In 2016, the church defrocked three Salvadoran priests after they were found guilty of sexually abusing children.
This year, it defrocked another following a canonical process in which the priest confessed guilt; he was also convicted in a Salvadoran court and sentenced to 16 years in prison.
The abuse scandals came to light in November 2015 when the San Salvador archbishop dismissed a priest accused of raping a girl over nearly a decade.