The fatalities were identified as Gladzin Himpiso, 10; Rona Mae Causing, 18; and and Dima Causing, 62.
The military initially reported 10 dead but regional commander Lieutenant Colonel Benjie Hao later revised the death toll.
The bomb went off on the Rural Transit bus as it pulled into a terminal in Carmen town in North Cotabato province at 10:40 a.m., said Cotabato police chief Cornelio Salinas.
Police identified the wounded as Guiariah Danggo, Marvin Marvicnal, Basilisa Aninipot, Sonny Balanag, Leo Limsiano, Alvin Diaz, Lovina Ayco, Lea Faviona, Analyn Suyco, Demia Causing, Hara Janine Cosca, Allan Himpiso Sr., Allan Himpiso Jr., Judy Ann Sumaylon, Ezleta Luneza, Rosa dela Garbo, Alberto Isidro, and Jenny Bergonia.
Among the wounded are children aged 6 and 11 years, said military officer Colonel Leopoldo Galon.
Salinas said a baggage containing the improvised explosive device was placed at a compartment of a Rural Transit bus by a still unidentified passenger.
The bus (body number 2922) was bound for Cagayan de Oro City from Tacurong City when the bomb went off on a national highway in Carmen.
The slain passengers were seated in the area where the bomb was planted, the police officer said.
Injured passengers were immediately rushed to Kabacan Medical Specialist Center in Kabacan, North Cotabato, and North Cotabato Provincial Hospital at Amas Complex in Kidapawan City for treatment.
The Wednesday blast was the second attack against Rural Transit Bus this year, police records show.
On February 7, an improvised bomb went off while the bus was in transit along Kabacan-Carmen highway. One passenger was injured during the blast.
Salinas hinted extortion as the motive behind the blast.
“We saw here a pattern. The suspects would board the bus from Tacurong City-Carmen highway and the blast would happen from Kabacan-Carmen highway,” he said.
The bus company, according to police, had been receiving extortion threats from several armed lawless groups, including the notorious Al Khobar, an extortion ring that allegedly has links with a terror group operating in southwest Mindanao.
Police were verifying Al Khobar’s link to the latest attack targeting the Rural Transit bus company.
Galon said extortion gangs linked to Muslim rebels have been suspected in previous attacks targeting bus companies in the region.
Presidential spokesman Edwin Lacierda on Wednesday expressed Malaca?ang’s condemnation on the latest bomb attack.
“Any act of violence against the civilian population is an act that is always condemnable and certainly we will look into the incident,” he said in a news briefing, adding the police are now investigating the incident.
Lacierda said Malaca?ang would ask Local Government Secretary Jesse Robredo on the possible assistance that could be extended to the victims.
In 2010, a bomb at the same terminal in Carmen killed one man and wounded two others, and a month before that, 10 passengers died in a bomb blast targeting the same bus company.
Muslim rebels and criminal gangs are behind decades-long unrest in the southern Philippines, home to minority Muslims in the predominantly Christian nation.