The M/V Esperanza Star, which was carrying 65 passengers and 55 officers and crew members, caught fire while sailing from Siquijor island in the south to nearby Bohol island, the coast guard said.
Coast guard firefighters onboard another vessel used a water canon and declared the fire out by around 0200 GMT (2pm NZST), a spokesperson said. The cause of the fire is still unknown.
Two coast guard vessels involved in firefighting and rescue operations were still in waters in the vicinity of the fire. The whereabouts and conditions of the rescued passengers and crew members were not disclosed.
The Philippines, an archipelago of more than 7,600 islands, has a poor record for maritime safety, with vessels often overcrowded and many ageing ships in use.
In March, a ferry carrying about 250 people also caught fire in southern Philippines, leading to the deaths more than two dozen people including a six-month old baby.
