The fire has reached Task Force Charlie at 10:06 a.m. and was placed under control at 10:39 a.m.
University officials said the fire affected the building that houses the College of Arts and Sciences and the College of Engineering and the Chapel.
The university said no one was hurt in the incident but television report said a firefighter was injured.
"The cause of the fire is still under investigation. The estimated damage to property is still being determined," UE-Manila said on its official Facebook account.
UE Manila and its other campuses were placed on heightened security alert "to ensure the safety of everyone in the UE community".
The university said UE Manila will be closed to students and visitors on Monday, April 4.
"All other UE campuses (UE Caloocan, UERMMMCI and the UE Annex Building) will be open. We will post a new advisory on Monday as to when UE Manila would reopen," the university said. (Sunnex)