The Vatican has released details of the letter was which sent in December.
In the letter, the pontiff speaks of the sufferings experienced by children within the Church and described it as a "sin that shames us all".
He added: "Let us find the courage needed to take all necessary measures and to protect in every way the lives of our children, so that such crimes may never be repeated.
"In this area, let us adhere, clearly and faithfully, to 'zero tolerance'."
The Catholic Church has faced legal action in various countries across the world for failing to protect children.
The Vatican also opened a commission for the protection of minors to introduce better safeguarding measures.