Top executives at the federal Department of Health and Ageing shared a $5.7 million performance bonus in the 12 months to June last year.
Staff at the department were told last week that it planned to cut 400 jobs as it struggled to rein in its spending in response to the latest increase in the Labor government's efficiency dividend.
But an analysis of recent departmental annual reports shows that the number of senior staff on salaries of more than $240,000 grew from 39 in 2011 to 53 last year.
The department's highest-paid worker got a pay rise of nearly $120,000 in the same period, taking their salary to $476,000 as at June last year.
The figures for the past 12 months are not yet available but a department official said on Friday the numbers were likely to be similar to 2011-12.
Department secretary Jane Halton, told 5200 workers the department needed to reform its structure to have fewer bosses and more rank-and-file workers.
The 2011-12 annual report shows 622 workers, mostly senior staff on individual agreements, were paid a total of $4,024,903 in ''performance-based bonuses'', payments above their normal salary and extras.
The department's 156 ''senior executive staff'' were paid $1,714,994 in bonuses in 2011-2012.
The annual reports also reveal that, in 2011, six of the department's employees were paid more than $240,000, a figure that had grown to 48 a year later.
Ms Halton, the highest paid person in the department, saw her salary grow from $355,857 in 2011 to $476,149 last year.
A spokeswoman for the department said the latest figures were being prepared and that a concerted effort was being made to cut back on the department's more highly paid staff. Health has more than 2000 executives at levels one and two and more than 150 senior executives.
''The details for the department's 2012-13 annual report are being finalised,'' the spokeswoman said.
''Whilst bonuses paid are likely to remain similar to previous financial years, we expect to see a reduction in the number of higher salaried employees.
''The department is taking the following actions to improve our APS (junior to mid-ranking) to EL (executive-level) ratio.
''As positions need filling, roles are carefully assessed against work-level standards to ensure they are at the appropriate level.''
She said ''business processes'' would also be reviewed to make sure salaries were justified by duties and executive-level jobs would be reassessed to make sure all executives in non-specialist jobs were actually managing people.
The spokeswoman said the department had not followed the lead of other federal departments and rolled executive bonuses into wages.
''This department has not rolled performance pay into base salaries where many other APS agencies have,'' she said.
''Executive-level employees have appeals rights for performance bonuses under section 33 of the Public Service Act.''