Aer Lingus chief executive Christoph Mueller saw his combined pay, bonus and pension rise by 4 per cent to almost €1.3 million last year.
According to the airline's annual report, Mr Mueller's basic salary was unchanged at some €475,000, while his bonus rose to €647,000. The company's pension contribution on his behalf was some €119,000 and other benefits amounted to €52,000 - bringing his total package to some €1.29 million.
The airline's finance director Andrew McFarlane saw his pay fall by 23 per cent last year to €876,000.
Mr McFarlane received a basic salary of €330,000, a bonus of €339,000, a pension contribution of €107,000 and €40,000 in other benefits.
The report attributed the reduction in Mr McFarlane's salary to a "voluntary arrangement".
The annual report shows that Aer Lingus chairman Colm Barrington was paid €126,000 last year, the same level as in 2011.
In total, the company paid its non-executive directors €514,000 in 2012 compared with €472,000 in the previous year.
The bonus paid to Mr Mueller represented 136.2 per cent of his salary while Mr McFarlane’s was 120.9 per cent.
Aer Lingus last month published preliminary results for 2012 which showed revenues at the airline grew by more than 8 per cent to some €1.393 billion.
It posted an operating profit of €69.1 million for 2012 as opposed to €49.1 million a year earlier. However, exceptional costs of €26.5 million dragged down its pre-tax profit to €40.6 million, roughly half the level of 2011.