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The International Union of Superiors General, which represents female Catholic religious orders around the world, denounced in November what it called the "culture of silence and secrecy" in the church that kept nuns from speaking about abuse.
"I think it's still taking place because it's not as though the moment you become aware of something it goes away".
"Pray that this goes forward", Francis said.
The LCWR, which represents about 80 percent of Catholic sisters in the USA, said it was grateful Francis had "shed light on a reality that has been largely hidden from the public and we believe his honesty is an important and significant step forward".
The issue of the abuse of nuns was raised in a Vatican magazine article published last week which detailed reports of sexual abuse by clerics resulting in nuns having abortions or giving birth to children fathered by priests.
What did Pope Francis say?
POGGIOLI: He did not name the order, but a Vatican spokesman said it was the French order Contemplative Sisters of Saint-Jean.
"There have been priests and also bishops who have done that, and I believe that it may still be being done", Francis said of the sexual assault of nuns.
The Leadership Conference of Women Religious also appealed in a statement for reporting guidelines to be established so abused nuns "are met with compassion and are offered safety".
A day after Pope Francis created an global uproar by saying Catholics nuns had been subjected to "sexual slavery" by the founder of a French order, the Vatican sought to clarify his remarks.
In 2013, the community publicly acknowledged that its founder, the Rev. Marie-Dominique Philippe, "sometimes made gestures contrary to chastity", with several women under his spiritual direction, according to La Croix, a Catholic newspaper in France.
Francis's admission of the problem was "the umpteenth blow to the church's image, but also an occasion to show that change really is underway", Scaraffia said.
Studies and investigative reports dating back to the 1990s revealed that nuns have suffered sexual abuse at the hands of male clergy in Africa, Asia, Europe, and South America, with African clergy in particular targeting nuns in order to avoid HIV transmission from prostitutes.
After the cardinal became pope, he reopened the investigation and dissolved the order, Pope Francis said.
One nun said last year that an Italian priest forced himself onto her when she was recounting her sins to him in a university classroom around 20 years ago.