Monsignor Dario Vigano – who has carried out sweeping reforms of the Vatican's media operations – stepped down over the row that has become known as “lettergate”.
The 55-year-old was accused of manipulating a private letter by Benedict XVI to help publicize part of the celebrations marking Francis' five years as pope.
At a presentation on March 12th of a collection of books on Francis' theology, Vigano read a letter from Benedict XVI praising the “deep philosophical and theological training” of his successor.
While Benedict XVI's tenure as pope was perceived to be more doctrine-focussed, Francis' more pastoral approach has riled some of the more conservative factions within the Catholic Church.
Nevertheless, in his letter, Benedict hit out at what he saw as the “foolish prejudice” of those who suggested that Francis was “a practical man without any particular theological or philosophical education”.
The press release from the event similarly featured Benedict's praise for the current pontiff, as if the letter was written for the anniversary.
But it turned out that Benedict's letter was in fact simply a private response from a month earlier to a request to review the 11 volumes in the collection. And in his response, Benedict actually said he would not have time to write the review.
In the final section of the letter, Benedict also criticised the Vatican's choice of German theologian Peter Hunermann to write one of the volumes of the Theology of Pope Francis. The retired pontiff, also a German, accused Hunermann of leading “anti-papal activities” during his eight-year papacy.
Following the presentation of the books, the Vatican published a photo of Benedict's letter, but only of the first page containing his praise of Francis.
The first two lines of the part containing his refusal to write a review were blurred to make them illegible.
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The row raged for several days, eventually forcing the Vatican to publish the entire letter on Saturday.
This led to Vigano's resignation on Wednesday, which Francis accepted in a letter.
“After carefully reflecting and thinking over the reasons for your request… I respect your decision and I accept with some difficulty your resignation,” Francis wrote.
Vatican observers nevertheless sought to play down the affair.
Greg Erlandson, editor of the independent Catholic News Service, said the incident sounded “more like a matter of poor judgment than deception” on the part of Vigano.
He pointed out that, at the book presentation, Vigano had read out the lines that were subsequently obscured in the photo. “For those who attended the news conference, the context of Pope Benedict's comments was clear,” he said.
Nevertheless, Vigano's attempts to reform the Vatican's media operations were not appreciated by everyone, said Vatican expert Marco Politi.
Vigano “is paying not just for his error, but also for the internal war that has broken out due to his impetuousness and the battle caused by his reforms,” Politi told AFP.
Vigano is a former director of the Vatican's official TV station, CTV (now called Vatican Media), and was appointed as prefect of the newly-established Secretariat for Communication in June 2015.
He was entrusted with cost-cutting and modernising the Church's media output and brought the previously disparate strands of the Vatican's media operations – TV, radio and newspaper Osservatore Romano – under his command.