Manila passenger Daryll Delgado said she had managed to rebook her flight for a later date after a "frustrating" experience.
An AFP reporter in the southern city of Davao said travellers were advised not to go to the airport but many only found out their flights had been cancelled after they arrived to check in.
More than 360 flights in and out of Manila were cancelled, diverted or delayed, affecting around 56,000 passengers.