ROME — A Vatican department has closed an inquiry into the alleged sexual abuse of a boy at an Opus Dei school in northern Spain, just weeks after a local newspaper published a handwritten letter signed by Pope Francis promising the accusations would be investigated.

The Vatican’s powerful Congregation for the Doctrine of the Faith, the doctrinal agency that also has primary responsibility for handling abuse cases, sent a letter to the Gaztelueta school in Bilbao dated Oct. 9 confirming that the probe had been concluded in favor of the teacher and the school.

The congregation cited a lack of evidence as its reason for closing the probe, and said that the “good name and reputation of the accused must be restored.”

In turn, the school issued a statement Monday including portions of the letter sent by the Congregation for the Doctrine of the Faith, and asserting that it was Pope Francis himself who made the decision to close the investigation.

“The headmaster’s office of Gaztelueta, makes public that it has received a notification of the firm decision by Pope Francis to conclude the case of alleged abuses by a former teacher of this school,” said the statement published on the institution’s website.

Leticia de la Hoz, a lawyer representing the family of the alleged victim, told the media in Spain that the family was “shocked” over the news, since as far as they know, no investigation was ever conducted.

A source with knowledge of the case, however, who asked not to be identified because he’s not authorized to speak on the subject, told Crux on Tuesday that local Church personnel delegated by the Vatican to run the investigation did speak to the victim and to family members.

On Oct. 3, the Spanish newspaper El Mundo published Francis’ initial letter, which was dated Dec. 29, 2014, and addressed to the father of the 20-year-old who claimed to have been abused between 2008 and 2010 by an official at the school.

The official is a lay member of the Catholic organization Opus Dei and is technically known as a numerary.

The papal letter was a response to one sent by the alleged victim’s parents, who also sent a series of documents which they claimed supported their son’s accusations.

“The cross is very hard. I ask Our Lord to help you carry it,” the pontiff wrote.

“In addition, today I am sending the documentation to the Congregation of the Doctrine of the Faith so that the teacher can face canonical proceedings without the young man being disturbed,” Francis wrote.

The school’s statement claiming vindication said that the Vatican’s conclusion was reached following an “extensive investigation,” which it claimed included evaluating several public and private documents as well as first-hand testimony from several people.

In a letter addressed to all the families in the school, headmaster Imanol Goyarrola said that the Vatican’s probe confirms what their own investigations had already shown, adding that this is the fourth time a probe into the accusation had ended because of insufficient proof. The other investigations were carried out by three regional authorities in northern Spain.

A Vatican spokesman wasn’t able to either confirm or deny that that case had been closed when asked about it during a briefing on Monday.

“Normally, the Congregation for the Doctrine of the Faith doesn’t make statements over individual cases,” said Rev. Federico Lombardi on Monday. “The normal procedure is for it to inform the people or the authorities involved.”

“I have no reasons to doubt what the headmaster said,” Lombardi said.

This is not the first time Pope Francis requested an expedited investigation into alleged sexual abuse by Church personnel after receiving a letter.

Last November, a similar papal intervention led a Spanish court in the southern city of Granada to charge 10 priests who were accused of being part of a clerical sexual abuse network.

However, in February the court dropped charges against nine of those priests because their alleged crimes fell outside the statute of limitations.