Mr Joyce's "reported" 2010-11 package rose 71 per cent to $5.01 million, but his "vested" remuneration what Qantas says he was actually paid fell 9 per cent to $3.04m.
The figure included a fixed salary of $2.05m, which was up from $1.96m.
The airline said the $5m figure was what it was required to report under accounting standards that call for some items to be costed, even though the value was not realised.
This included, for example, shares awarded but not vested.
It said the vested remuneration included fixed pay, cash bonuses paid and the value of shares and rights vested during the year.
"Mr Joyce's salary is not excessive compared with other large Australian companies," a Qantas spokesman said. "His actual salary in 2010-11 was 9 per cent lower than last year and Qantas executives have not been awarded a cash bonus for the past two years."
