Philippines President Gloria Macapagal Arroyo met her cabinet overnight to discuss tightening security in the wake of the blast, the third in two days.
The Philippines has been hit by a wave of bomb attacks in the past two weeks, in which more than a dozen people have died.
On Thursday, seven people were killed and more than 100 injured in two bomb explosions in the mostly Christian city of Zamboanga in the south.
The Defence Ministry said the Zamboanga attack was probably carried out by the separatist Abu Sayyaf group, once linked to Osama Bin Laden's al-Qaeda network.
Debris examined
Police say they do not yet know who planted the bomb on board the Golden Highway bus.
"This was definitely an act of terrorism," said National Security Advisor Roilo Golez.
Explosives experts are examining the remains of the bus to try to determine the type of device used in the attack.
Police said the bomb was placed under a row of seats at the back of the bus.
At first, more than two people were thought to have died, but there was some confusion because of the state of dismembered bodies.
Terrorism vow
President Arroyo was due to meet officials in Manila on Saturday to discuss the security situation, said Mr Golez.
On a visit to Zamboanga on Friday, the president said the bomb attacks had gone from "bad to worse" and urged Filipinos to help fight terrorists.
"Terrorism cannot survive for long in an unfriendly environment," she said.
Police said the Zamboanga attacks bore the hallmarks of the Abu Sayyaf guerrillas, but would not speculate if the group was suspected of carrying out the Manila bus bombing.
Abu Sayyaf recently threatened attacks in retaliation for a military offensive against it.
It has been blamed for another bombing in Zamboanga on 2 October that killed four people, including an American Green Beret commando.