A coast guard vessel has been deployed to rescue the people on board and extinguish the blaze.
The M/V Esperanza Star caught fire early in the morning as it was traveling from Siquijor province to Bohol province in the central Philippines, the coast guard said.
The coast guard released photographs and a video of the burning ferry that shows flames and black smoke billowing from two decks at one end of the ferry.
None of the 65 passengers and 55 crew members could be seen aboard.
(Photo: Philippine Coast Guard)