Around 100 clerical staff will have their wages docked for a brief unofficial strike earlier this month.
The Irish Times reported that in a letter sent to Siptu union president Jack O'Connor, Aer Lingus chief executive Dermot Mannion said the pay of "all staff involved in the stoppage will be deducted for the period of the stoppage".
The clerical staff's action began just before 6am on Saturday morning and lasted for about an hour. It related to staff being asked to work on check-in desks and at boarding gates. No notice of the stoppage was given to Aer Lingus by the workers.
The airline has also informed Siptu that the company planned to launch an investigation into the stoppage, which could lead to disciplinary action being taken.
The investigation begins today. "This . . . may lead to disciplinary action," Mr Mannion said.
The stoppage directly affected 23 early-morning flights. As a result, nearly all of Aer Lingus's short-haul flights that day were delayed.
In a strongly-worded letter, Mr Mannion said the action by Siptu members had shown "complete disregard" for the airline's customers. Mr Mannion said the unofficial action was "all the more disappointing" given the competitive pressures that the airline faces, particularly from Ryanair.
"Our main competitor at Dublin airport [ Ryanair] does not recognise trade unions and as such has a staff cost base that gives them a consequent competitive advantage," Mr Mannion said.
Aer Lingus and Siptu are currently in negotiations, under the auspices of the Labour Court, in relation to the airline's plans to change work practices in a bid to achieve cost savings of €20 million a year.
In a separate letter to Siptu's national industrial secretary Michael Halpenny, Mr Mannion said he wanted to implement these changes by August 1st.
Siptu said it would reply to Mr Mannion's letters today. The union said the stoppage by its members last weekend had not been sanctioned by the union.