In Valenzuela City in the Manila area, police said, two people were killed after a wall collapsed, the Philippine Daily Inquirer reported.
Flooding also led to cancellation of some classes, closing of government buildings, including courts, and heavy traffic on major roads, the Inquirer said.
The Ipon Dam opened two gates Tuesday morning after water reached a critical level.
La Mesa Dam in Quezon City was on red alert Tuesday.
The National Disaster Risk Reduction and Management Council said Tuesday water levels in several riverways were nearing critical spill levels.
The Rosario Junction riverway had four flood gates open and its water level was about a few yards below the critical spill level.
The San Juan River was about 3 feet above its critical spill level.
Seven domestic flights were canceled as a result of the weather.