The Pontiff spoke with reporters aboard the Papal plane en route to Abu Dhabi in the United Arab Emirates, where he is due to become the first Pope to visit that nation's increasing Catholic population made up mostly of guest workers from the Philippines and from India.
Francis said the problem could be found "anywhere" but was prevalent in "some new congregations and in some regions". Women are [seen as] second class, and it starts from there.
A January meeting of US bishops came and went without any discussion of the sexual abuse problem dogging the Church.
"There have been bishops and priests who have been doing it and I believe it may still be being done", he said.
He said the Catholic Church "shouldn't be scandalized by this", adding that "there are steps in a process", and "we are working on it".
The Saint Jean order was dissolved in 2005, the first year Pope Benedict served as the head of the Church.
The Church has "suspended several clerics" and the Vatican has been 'working (on the issue) for a long time, ' he said.
Pope Francis attends the Easter Mass at St. Peter's Square on April 1, 2018 in Vatican City, Vatican. "But it's a path that we have already begun", Francis said while returning home from the United Arab Emirates. It also alleges that reports of priests abusing nuns in Africa were filed to the Vatican in the 1990s and that nothing was done.
As well as causing untold pain to the victims and their families, he said "the Church's credibility has been seriously undercut and diminished by these sins and crimes, but even more by the efforts made to deny or hide them".
The Associated Press also previously reported that the Vatican was well aware of the existence of sexual misconduct against nuns at the hands of priests but has done nothing to end it.
In November, the International Union of Superiors General, which represents all female Catholic religious orders, publicly decried the "culture of silence and secrecy" that prevented nuns from reporting abuse and encouraged sisters to report assaults.
Pope Francis added: "Pray that we can go forward, I want to go forward".
The issue was brought to light after the February issue of a monthly woman's magazine, which is distributed alongside Vatican newspaper L'Osservatore Romano, was published.
All the nuns who have been served a transfer notice have formed a support group for a fellow nun who alleged a year ago that Bishop Franco Mulakkal had raped her 13 times between 2014 and 2016.