Airline officials said 8 flights were cancelled while 4 others had to be delayed Sunday. Nine flights were cancelled while 4 others were cancelled on Saturday.
The company said it did not expect a surge in the number of passengers in October.
Airphil Express has 20 pilots but they have all exceeded their quota in flying hours, company spokesperson Maria Jaha said.
Airphil Express addressed the crisis by borrowing the pilots of sister company Philippine Airlines.
Some passengers eventually got on board an Airphil Express aircraft and left for the provinces on Sunday after hours of waiting.Others, meanwhile, were forced to rebook their flights.