Zamboanga City Mayor Isabelle Climaco-Salazar said the suspension of classes in the city covers all levels.
The mayor also called off work in government offices that are not involved in frontline services.
She added rescue teams were deployed to the city's flooded areas as early as 3 a.m., with barangay officials told to use the five-percent calamity fund to assist residents.
The city government also advised people along riverbanks and low-lying areas to "seek safer grounds while weather condition remains abnormal."
Meanwhile, some flights to and from Zamboanga were also cancelled due to bad weather.
The Civil Aviation Authority of the Philippines (Caap) suspended flights to and from the Zamboanga International Airport due to flooding at the airport's runway.
CAAP also issued a Notice to Airmen barring flights to and from the airport from 9 a.m. to 9 p.m., radio reports said.
CAAP was set to issue another Notice to Airmen on Wednesday to signal if it is clear to resume flights at Zamboanga City International Airport.
Meanwhile, the Office of Civil Defense also said many roads in Zamboanga City were not passable to vehicles Tuesday morning due to floods brought by heavy rain.
Eric Castillo of OCD Region 9 said vehicles were stalled along Pilar Street due to the floods.
Many families were also evacuated from their homes in districts like Divisoria due to the floods while the Philippine Coast Guard and Philippine Navy helped in the evacuation.
Zamboanga City has yet to recover fully from the effects of last month's fighting between government and Moro National Liberation Front forces