Speaking on board the papal plane back from the United Arab Emirates, he argued the phenomenon was rooted in society's mistreatment of women, and that nuns need a safe space to speak out about abusers.
The pope said ongoing sexual abuse problems have mostly been in "certain congregations, predominantly new ones and in certain regions more than others".
Last week, Women Church World - the Vatican's women's magazine - denounced the sex abuse and said that in some cases sisters were required to abort priests' unborn babies that were born as a result of rape.
Recently more nuns, encouraged by the MeToo movement, have been coming forward to describe abuse at the hands of priests and bishops. He added that "I think it's still going on, because it's not something that just goes away like that".
"Francis told reporters on his flight that 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.
Editor Lucetta Scaraffia said that Pope Francis' addressing of abuse "can be of some help" but that the church had to recognise the issue as a whole. "We have suspended some priests because of this", he said.
"Pray that this goes forward", he said of the Vatican efforts to fight it.
Pope Francis has summoned key bishops from around the world to a summit later this month at the Vatican to find a unified response on how to protect children from sexual abuse by clergy. In January 2018, he dismissed accusations that Chilean bishop Juan Barros had covered up sexual abuse committed there by a priest named Fernando Karadima.
In a separate case in India previous year, a bishop was arrested over allegations that he raped a nun 13 times between 2014 and 2016.
Although it was not confirmed officially by the Holy See, Francis' story has echoes of reports about Cardinal Joseph Ratzinger's attempts to take action against the Legionaries of Christ founder, Fr Marcial Maciel, who turned out to be serial sexual abuser of seminarians.
The faithful greet and take photos of Pope Francis, center left, as he arrives for the weekly general audience on February 6, 2019 at Paul-VI hall in the Vatican.