A military spokesperson said the Bangsamoro Islamic Freedom Fighters (BIFF), a band of a few hundred guerrillas operating on the troubled southern island of Mindanao, are believed to have staged Tuesday's attack, which also left 42 wounded.
The BIFF denied involvement.
The bomb was similar to one used in a November attack on another vehicle belonging to the same bus company, which the BIFF is also believed to have orchestrated, said Major Ezra Balagtey, spokesperson for the region.
"The bomb/IED is made of an 81 mm mortar round (that was) cellphone-activated. The same bomb signature with the IED explosion that happened last November," Balagtey said in an SMS message to journalists.
BIFF spokesperson Abu Misry Mama denied the charges.
"Bombing civilians would not benefit us. The (military) is fabricating stories again to malign us," he said.
A spokesperson for President Benigno Aquino condemned the bombing.
"We condemn the violent act that resulted in the loss of lives," said Abigail Valte.
Valte did not say who the president's office believed was responsible although she said authorities were following undisclosed leads.
It was the latest attack on the bus company which operates in Mindanao, where rebels and other armed groups are active.
Aside from the November bombing, 10 people were killed when a bomb exploded aboard a bus belonging to the company in 2010. That incident was blamed on an extortion scheme linked to extremists.
The BIFF split from the main rebel group, the Moro Islamic Liberation Front (MILF), in 2008.
It opposes the peace deal between the 10,000-strong MILF and the government signed in March, and vows to keep fighting for a separate Islamic state in the south of the largely-Christian nation.
In August the BIFF uploaded clips on YouTube showing one of its leaders pledging support for the Islamic State organisation, the brutal group that has seized a large swathe of territory in Iraq and Syria.
Rommel Banlaoi, chairperson of the Philippine Institute for Peace, Violence and Terrorism Research, said it was likely that the BIFF carried out the latest bombing.
"The BIFF is fully engaged in offensive military operations. They are heightening their military activities right now, even their bombing operations," he told AFP.
"Their bombing activities are commonly mixed with their criminal activities (such as extortion)."
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America and India is behind this........this is a conspiracy to defame.....?