The backpack containing the alleged bomb was found to hold nothing more than dirty clothes and other assorted items, the police investigator handling the case said.
"It was just old clothes and junk. The bomb report was negative," he told AFP.
The backpack was hurled by a man on an overhead footbridge onto the roof of a passing commuter bus on Manila's main thoroughfare at about 5pm. The bus driver halted the vehicle and summoned the police, who stopped traffic on both sides of the highway, causing a massive traffic jam that stretched for kilometres (miles).
A bomb-sniffing dog sent in by the police was seen sitting by the bag, indicating that it had smelled explosives.
However an x-ray of the bag could not find any detonator and an explosives expert later confirmed there was no bomb.
Valdez said a witness reported that the bag may have been hurled onto the bus during a botched robbery as the owner and a suspected thief were struggling over it.
He did not believe the incident was intentional attempt to cause panic, but said the owner of the bag has yet to be located.
Four hours after the road was closed, vehicles were allowed to pass the thoroughfare once more.
Commuter buses in the Philippines have been bomb targets in previous years, either by extortionists or Muslim extremists.
Just last month, three people were killed when a bomb exploded aboard a bus amid fighting with Muslim guerrillas in the troubled southern city of Zamboanga
