Pilots employed by a Qantas subsidiary Network Aviation walked off the job for 24 hours on Wednesday.
Perth Airport's website listed more than 40 flights to regional towns and mine sites as cancelled.
The protected industrial action was expected to impact thousands of fly-in fly-out workers, with BHP, Rio Tinto, Fortescue Metals Group and Woodside Energy forced to take measures to minimise the disruption to their operations.
This included cancelling non-essential travel, rescheduling travel to other days and booking charter services with other aviation companies.
Earlier in the week, Qantas confirmed that it was scrambling to find alternatives for customers, including rerouting Qantas 737 jets, using aircraft from other operators and rescheduling flights.
Wage negotiations between Network Aviation and its pilots have been at a standstill since March, with more than 200 pilots affected.
Network Aviation operates more than 500 flights per week, flying the resource sector's FIFO workers to and from regional towns and mine sites across WA.
There are estimated to be more than 60,000 FIFO workers in WA who fly into remote work sites for mining, oil and gas projects across the state.
