Virgin Australia boss John Borghetti's take home pay fell by less than two per cent to $2.66 million last financial year, despite the airline falling to a $98 million loss.
Mr Borghetti's remuneration in the 2012/13 financial year was $46,000 less than what he was paid in the previous year, when the airline made a $22 million profit.
The CEO's short term bonuses in 2012/13 were cut by $362,000 to $794,000 because of the company's weaker performance, but that was mostly offset by an increase in his base salary.
A salary increase of $350,000 to $1.65 million was made in recognition of Mr Borghetti's efforts to overhaul the company's business model, the Virgin Australia annual report, released on Friday, showed.
Those changes, including an update of the look and feel of the airline, a stronger passenger loyalty program and increased access to global markets, was delivered ahead of schedule.
The airline's 2012/13 loss was attributed to a difficult economic and competitive environment, one-off restructuring costs, and the carbon tax.
Mr Borghetti's annual pay was lower than his rival, Qantas chief executive Alan Joyce, who received $3.3 million in 2012/13.
