The Pontiff's comments, during a ceremony at the Sistine Chapel to commemorate the baptism of Jesus, came one year after a similar message he gave at an equivalent event last year.
He was quoted by the AFP news agency as saying: "The ceremony is a little long, someone's crying because he's hungry. That's the way it is.
"You mothers, go ahead and breastfeed, without fear. Just like the Virgin Mary nursed Jesus."
Pope Francis baptised 15 boys and 13 girls during the service on Sunday.
On a visit to the parish of St Joseph in Rome two years ago, he criticised people who say babies who cry during church should be asked to leave.
He said: "Babies cry, make noise, go here and there. But it annoys me when a baby cries in church and there are those who say he needs to go out.
"The cry of a baby is God's voice: never drive them away from the church!"