The suspects will reportedly be flown to Manila today to be presented to President Arroyo and Philippine National Police chief Director General Hermogenes Ebdane Jr.
Police sources said the five suspects are members of the Abu Sayyaf.
Details of the arrest are not yet known but investigators are said to have a "very strong case" against the suspects.
The first terrorist bombing occurred in a restaurant in Zamboanga City’s Malagutay district last Oct. 2, killing an American serviceman and three Filipino civilians.
In the second attack, seven people were killed and 150 wounded when a powerful blast ripped through two department stores on Oct. 17 in the city’s commercial center.
Last Sunday night, a Philippine Marine was killed and 18 people were wounded after a bomb exploded in front of Fort Pilar, a Catholic shrine in Zamboanga City.
Earlier yesterday, Ebdane said police would arrest "within 24 hours" five suspects in the Zamboanga City bombings.
"We have identified them but we still have to arrest them," he told the Federation of Filipino-Chinese Chambers of Commerce and Industry in Binondo, Manila.
Zamboanga City police said the chemical used in the Fort Pilar bombing was similar to the one used in the attack on a restaurant in Malagutay.
Chief Inspector Antonio Clarito, operations chief of Zamboanga City police, said bomb experts are examining the shrapnel found at the scene to detect the type of explosives used to make the bomb.
The bomb that exploded in Malagutay weighed around a kilo and contained "brownish" explosive which could be a concoction of gunpowder and TNT, police said.
Meanwhile, police are looking at the possibility that the Abu Sayyaf, Moro Islamic Liberation Front and former members of the Moro National Liberation Front are behind the spate of bombings in Zamboanga City and Metro Manila.
"These (bombings) were launched when the government has an offensive against terrorist groups," said a military official, who asked not to be named.
On the other hand, police sources said the bombers might be getting support from foreign terrorist groups like al-Qaeda and Jemaah Islamiyah.
"There is a pattern that we see and we are trying to establish these with the series of explosions to the events and other incidents that happened in Southern Mindanao and Metro Manila," sources said.–Jaime Laude, Mike Frialde, Roel Pareño, Christina Mendez, Marvin Sy