Members of the Central Police Districts Special Weapons and Tactics (SWAT) team and the Ordnance and Explosive Division found no bombs in the building or its surrounding area.
Police said the phone call was received by Sheryll Villanueva, a clerk of QC-RTC Branch 217 at about 7:30 a.m.
Villanueva told investigators that a male caller told her to leave the building because a bomb would be exploding in a few minutes.
She immediately informed building security, which sought assistance from police.
Senior Police Officer 2 Jaime Halog, who led the response team, said panic was minimal since the incident took place before office hours.
Earlier, four people were hurt after a pill box exploded near a mall on Commonwealth Avenue the other night.
Police identified those hurt as Luis Reyes, 20; Paul Abella, 47; Rodel Bautista, 27; and Herminia Torres, 35, a teacher.
All four were reportedly dining at Jacobs Grill located in front of the Ever Gotesco Mall.
Initial investigation disclosed that someone threw the pill box in the direction of the restaurant, aimed at a waiter with whom the suspect had a grudge.