Earlier this week three priests and a lay person in the city of Granada were arrested by police looking into the allegations.
It comes after Francis was sent a letter from a man who said he was a victim of the abuse.
"I read it. I called the person and I told him 'go to the bishop tomorrow' and then I wrote to the bishop and told him to start an investigation," the Pope told reporters.
He added: "I received this news with great pain, very great pain, but the truth is the truth and we should not hide it."
Spanish Interior Minister Jorge Fernandez Diaz told reporters the allegations were of a historic nature and investigations by police had started 'some time ago'.
Francis has spoke of his zero tolerance policy for abuse of children after several Church scandals in recent years.
