Father Ibrahim Faltas ruled out arson, saying a candle tipped over and set off a small fire that caused minor damage today.
Just two days earlier, Pope Francis visited the site during his three-day visit to the Holy Land.
The Church of the Nativity in the West Bank town of Bethlehem is built over the grotto where tradition says Jesus was born. It is one of the holiest sites in Christianity.
According to Christian belief, Jesus was born in Bethlehem, spent much of his life in Nazareth and the northern Galilee region of Israel, and was crucified and resurrected in Jerusalem.