Airline passengers travelling to or from parts of regional Australia could face significant delays if a pay dispute between Rex and the pilots' union isn't settled soon. 

Regional Express Airlines pilots have begun voting to decide if they will take protected industrial action.

Over the next six days more than 250 pilots who fly the Saab 340 fleet will take part in a ballot, approved by the Fair Work Commission last week.

The independently monitored vote will run until midday (AEST) on June 22.

The ballot follows a breakdown in negotiations between the Australian Federation of Air Pilots and Rex.

Still 'willing' to negotiate

A union spokesperson said that the recent pay deal was "worse than previous offers".

However, the spokesperson said, union members were still interested in avoiding industrial action if possible.

"The AFAP remains willing to continue negotiations with Rex to try and finalise the current enterprise agreement negotiations that have been ongoing for more than four years," the spokesperson said. 

The union will vote on a number of actions, including a possible four-hour work stoppage and bans on pilots signing on for work if their next shift is less than 10 hours after their previous one.

Regional cities, such as Broken Hill, could see the number of flights in and out of their local airport slashed by more than 90 per cent if Rex pilots go on strike.

Until recently Rex operated a monopoly in areas like far western NSW for most of the past two decades.

For cities like Broken Hill and Mount Gambier, Qantaslink's expansion will prevent the potential for a complete halt in flights, if a full strike by Rex pilots takes place. 

Regional Express Airlines declined to comment until the ballot had closed and a decision on industrial action had been made.