On Monday, Dermot Mannion, chief executive of the airline, called on relevant staff to assist in the screening, assessment and training of new captains and co-pilots in Belfast.
“It is important that you understand that if you fail to carry out your full range of duties, for whatever reason, you will be suspended from the payroll with immediate effect,” Mannion wrote.
Between 50 and 70 Aer Lingus pilots, out of its fleet of 490 pilots, could face suspension if the threat is followed up.
The dispute adds further to tension between workers and management, after the carrier announced a pay freeze for 3,600 employees as part of cost-cutting measures in the wake of increasing competition in the low-budget sector.
The Services, Industrial, Professional and Technical Union (SIPTU) said it had not ruled out industrial action, following talks with senior management.
Trade union Impact, which represents pilots, said the threat of suspension is counterproductive to both the company’s objectives and ongoing negotiations.
The airline has a history of hard-line human resources policies. In 2005 a leaked document exposed plans to make life so unpleasant for staff that they would volunteer for redundancy. Mannion took up the post of chief executive at the hight of the scandal, after his predecessor John Sharman was called to account by a committee of Irish MPs.