The issue hit the headlines last year after a nun accused an Indian bishop of repeatedly raping her in a case that triggered rare dissent within the country's Catholic Church.
Francis said the problem could be found "anywhere" but was prevalent in "some new congregations and in some regions".
"I think it's still going on, because it's not something that just goes away like that. On the contrary," he added.
He said the Church has "suspended several clerics" and the Vatican has been "working [on the issue] for a long time".
'Must do more'
"I don't want to hear it said that the Church has not got this problem, because it has.
"Must we do more? Yes! Do we want to? Yes!" he said.
He said it was a cultural problem, the roots of which lie in "seeing women as second class".
The February issue of "Women Church World", a supplement distributed with the Vatican's Osservatore Romano newspaper, warned that nuns have been silent over abuse for decades for fear of retaliation.
It said the Vatican received reports of priests abusing nuns in Africa in the 1990s.
"If the Church continues to close its eyes to the scandal - made even worse by the fact that abuse of women brings about procreation and is therefore at the origin of forced abortions and children who aren't recognised by priests - the oppression of women in the Church will never change," editor Lucetta Scaraffia wrote.
In the Indian case, Bishop Franco Mulakkal was arrested on September 21 in the southern state of Kerala on suspicion of raping the nun in question 13 times between 2014 and 2016.
Pope Francis suspended him the day before his arrest, appointing another bishop in his place. Mulakkal, 53, who headed the diocese of Jalandhar in the northern state of Punjab, has denied the allegations.
The nun first spoke out in June but police only started formal questioning in September, as fury over the case mounted.
Five nuns - in a rare public show of dissent within the Indian Church - and dozens of supporters staged days of protests.
Failure by Church officials to take action on sexual abuse allegations has been one of the biggest scandals to hit Roman Catholicism globally in recent years.