Police Superintendent Suharto Tocao said the blast occurred while the YBL bus was parked in the public terminal in Tacurong City in Sultan Kudarat province, 990 kilometres south of Manila.
"There were already no passengers inside the bus when the explosion occurred," Tocao said.
A 12-year-old vendor and two passengers who had just alighted from the bus were wounded in the explosion, but were out of danger.
Colonel Danilo Garcia, an army brigade commander, said the improvised bomb could have been made from a 60-millimetre or 81-millimetre mortar fitted with a triggering device.
He said the blast was quite powerful, tearing off the back portion of the bus.
Police said an extortion syndicate could be behind the bombing.
The explosion occurred a day after police announced the filing of criminal charges against two suspects in a similar attack in nearby Koronadal City last week.
"The bomb attack could be a demonstration of outrage by the group, whose two members had been arrested last week and charged in court," police Chief Superintendent Felizardo Serapio said.
Last month, eight people were killed in separate bombings of buses of a different company in Davao del Sur and North Cotabato provinces. Extortion was also being eyed in the attacks.//Deutsche Presse Agentur (DPA)