Departmental shifts and mergers in February 2020 meant some senior figures earned double-digit percentage increases to their remuneration packages during the 2019-20 financial year, inching closer to the million-dollar mark.

It was announced in April that an expected 2 per cent pay rise would be delayed for federal public servants by at least six months due to the COVID-19 pandemic.

But annual reports show the total cost of remuneration packages for a number of senior executive staff increased with some departments' budget lines stretching by more than 15 per cent.

A total remuneration package includes a base salary, superannuation, annual and long service leave entitlements as well as other negotiated benefits.

The Department of Finance's top remuneration package, awarded to secretary Rosemary Huxtable, reached $915,906 for 2019-20 - an increase of 11.5 per cent on the previous year. The total cost of senior management's remuneration package, which offers no bonuses, grew by nearly 10 per cent to $3.5 million for 11 roles.

A Finance spokesperson said the total KMP remuneration was caused by the addition of another position while the secretary's increase was "primarily driven by a reduction in the annual leave taken". None of the senior executives had received any increases since April.

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For the social services secretary, Kathryn Campbell, her remuneration package grew by 7.4 per cent to $850,918 while the total of the department's key management team totalled $3.2 million - an increase of 15.6 per cent.

Annual leave not being taken and changes to personnel were also provided as reasons for the increase by a department spokesperson.

It's important to note the departmental changes that occurred in February affected some of the total packages. Termination benefits for outgoing secretaries helped to push the top remuneration packages well beyond the million-dollar mark.

Martin Parkinson left his role as the Department of Prime Minister and Cabinet (PMC) secretary for Scott Morrison's former chief of staff Philip Gaetjens in September 2019. Mr Parkinson received a base salary of $168,147 with a termination payout of $880,414.The final package totalled $1.06 million, nearly $200,000 more than Mr Gaetjen's $860,366 for the year.

Similar termination benefits occurring in the Department of Industry, Innovation and Science, the Department of Infrastructure, Transport, Regional Development and Communications and Services Australia saw the new agencies also breaching the million-dollar mark.

The Department of Education, Skills and Employment (DESE) secretary Michele Bruniges kept her role after a recent merge between education and the former employment department, receiving a major pay bump for the extra responsibilities to $968,871 from $825,023. The senior executive team also grew by one person to 10 but the total remuneration package across those roles increased 37.5 per cent to $4.22 million.

It was other departments as well that faced remuneration increases despite no major changes in the makeup.

The Department of Defence's top package went to defence force chief General Angus Campbell, who received $1.06 million followed by the department's secretary Greg Moriarty with a little more than $950,000. General Campbell's package increase represented nearly $40,000, or 3.78 per cent, more than the previous reporting period.

Mr Moriarty himself gained a 7.72 per cent increase on his previous year, up nearly $70,000 to a $954,515 package.

Defence force members, like the APS, were also told in July their scheduled 2 per cent wage increase would be delayed from November 2020 to May 2021.

A spokesperson for Defence said the rises were mainly due to annual leave accruals caused by Bushfire Assist and the COVID-19 response.

Out of all the departments, veterans' affairs secretary Liz Cosson received the smallest package for 2019-20 at $752,864, a modest 2.76 per cent increase on the previous year, while DFAT secretary Frances Adamson earned the smallest increase of 0.34 per cent to a total $939,668 total package.

Chris Moriatis, the Attorney-General Department's Secretary, was the only department head to have faced a decrease in his package compared to the previous year.

During the 2019-20 period, Mr Moriatis received a $866,168 remuneration package, which marks around $12,000 less, or a minus 1.41 per cent decrease, on his 2018-19 remuneration package. The executive leadership team, however, stretched to a total remuneration package sum of $3.57 million across seven roles, including Mr Moriatis', representing a 10 per cent increase on the 2018-19 figures.

A department spokesperson explained this increase was principally caused by the addition of a new Deputy Secretary to deal with functions held by the the former Department of Jobs and Small Business.

Treasury and Health are expected to release their annual reports at the end of November.

Secretary packages are determined by the PMC secretary Mr Gaetjens in accordance with the Remuneration Tribunal Act.

A PMC spokesperson said only three secretary packages were adjusted with the changes that came into effect February 1, 2020 - the Department of Agriculture, Water and the Environment, the Department of Infrastructure, Transport, Regional Development and Communications and DESE.

The remainder of the senior executive team's remuneration packages are determined by the agencies or departments themselves.

"Remuneration arrangements for Key Management Personnel are the responsibility of each agency," a PMC spokesperson said.

"The Department of the Prime Minister and Cabinet is not aware of changes made for those offices across the Australian Public Service."

Of all the annual reports examined, all departments increased their total remuneration packages by at least 7 per cent with the exception of PMC, which decreased by 4.48 per cent on the 2018-19 reporting period.

Termination payouts distort some of the departments' increases but Finance, DFAT, Defence and the Attorney-General's Department all ranged between 7 and 11 per cent rises. Across only a handful of people, hundreds of thousands was given over the course of the year.