Virgin Blue is facing a backlash from flight attendants and pilots after an enterprise bargaining agreement was overwhelmingly rejected.

Pilot discontent about stalled negotiations over pay and working hours reached boiling point in February and led to warnings that Virgin Blue could be hit with its first ever strike.

Now, nine out of 10 flight attendants have rejected a new enterprise bargaining agreement after two years of negotiations.

The rejection came as Virgin Blue denied a shortage of pilots had led to flights being cut. Spokeswoman Heather Jeffery said the airline's pilot roster was running tighter because some were undertaking upgrade training.

Some pilots were also on annual leave and claims that a shortage was leading to cancellations were "a little imaginative", she said.

However, the Australian Federation of Air Pilots said: "There may be other reasons, but there is an intrinsic shortage of pilots."

The flight attendants voted 992 to 123 vote to reject the agreement on April 2 although their union, the Flight Attendants Association of Australia, had endorsed it. The union did not return calls on April 3.