Industrial action has been called by union Adedy even though a court has ruled it unlawful.
A 24-hour walk-out is planned on Wednesday.
If it goes ahead all scheduled flights could be affected.
The union wants the reinstatement of work bonuses which were previously scrapped.
A strike earlier this year caused disruption but this weeks action will likely cause more disruption ahead of the Easter period.
Airlines such as Aegean Airlines have begun offering free flight change waivers for Wednesday and flight credits for those who opt to cancel their booking.
The strike could still halted by the court, Aegean said.
Tags: air traffic controllers strike Greece, Aegean Airlines
