The salary package of the Australian Federal Police commissioner will jump by $100,000 to $650,000 after a sweeping review of the responsibilities of senior officials.
The director-general of ASIO will also have a $100,00 pay rise, from $500,000 to $600,000.
The Remuneration Tribunal says the pay rises for the mostly Canberra-based jobs will be phased in during the next 18 months.
The Australian Public Service Commissioner will enjoy a package of $600,000 a year.
The salary of the vice-chief of the Australian Defence Force will rise from $460,000 to $550,000 while the pay of the chiefs of the Army, Navy and Air Force will rise from $440,000 to $525,000.
The pay of the director-general of the Office of National Assessments increases from $450,000 to $525,000 and that of the Australian Electoral Commissioner from $400,000 to $500,000.
Running Old Parliament House will be worth $325,000 while the chief executive of the National Capital Authority will receive $300,000.
In June the tribunal proposed increasing the AFP commissioner's package to $600,000 but has settled on the higher figure, about $12,500 a week.
The average full-time worker, by comparison, earns $74,900, while the average federal bureaucrat earns $81,900.
The packages for top public sector positions are still well below those in the private sector, where the average chief executive of a top-100 ASX company earn a fixed pay of $2.1million, excluding bonuses.
CPSU Assistant National Secretary Louise Persse said the pay rises were too high in a sector characterised by budget cuts and meagre pay rises for staff.
''For a sector that's tightening its belt enduring job cuts, and that has worked hard to get three per cent pay rises, pay rises of this order are a bit much,'' Ms Persse said.
''We know these people have complex and demanding roles but, especially in light of the current environment, it's a matter of proportions,'' she said.
But the tribunal says the new pay rates should reflect the size and complexity of senior jobs. Salary scales should be simplified and should compensate for often onerous duties. ''Remuneration should be commensurate with current responsibilities, not based on past achievements or potential future challenges,'' the tribunal says in its latest ruling. ''The remuneration arrangements for the appointees to such positions will be lower than may be paid in the private sector, noting that the tribunal is conscious of the prestige, honour, power and influence attached to certain senior public offices.
''Nonetheless, the tribunal is conscious that remuneration must be at a level sufficient to attract and retain candidates of appropriate capacity.''
The tribunal proposed the new salary structure in June, noting then that many senior office holders were paid less than justified by their responsibilities.
''The structure eliminated the fine levels of differentiation between many offices that had developed over the years but could no longer be sustained logically,'' it says.