There was also no trading at the Philippine Stock Exchange and no clearing and settlement at the Securities Clearing Corporation of the Philippines, Xinhua reported.
Presidential spokesperson Edwin Lacierda said state employees involved in disaster risk reduction and management are not covered by the work suspension.
Airlines including Tiger Air and Cebu Pacific have cancelled several flights owing to inclement weather and roads leading to the airport were flooded. Authorities have issued a warning and said that the flood situation may continue for the next two days.
On Monday, most parts of Manila were flooded following heavy rains brought by tropical storm Trami.
Due to the floods, the government suspended classes at all levels in the capital and 12 northern provinces.