Nine of the 25 hostages, including three children, were released earlier, and appeared to be unhurt, Jorge Carino, a journalist from ABS-CBN, a Philippine TV-network, told Al Jazeera.
Former police officer
The hostage-taker, identified as Rolando Mendoza, is a dismissed police who was demanding that he be given back his job on the police force.
He was armed with an M16 rifle and small arms.
Two negotiators had approached the bus and spoken to the gunman who gave the negotiators a list of demands, local television reported.
Mendoza asked for food for the remaining 16 on the bus, which was delivered, and fuel to keep the air-conditioning going.
A handwritten note in bold letters talking of a "big deal" after 3pm (0700 GMT) was posted on the glass door of the bus, television images showed.
The note read: "Big deal will start after 3pm today," but the deadline passed without incident.
Later the note was replaced with another message saying: "Big mistake to correct a big wrong decision."