Australian Public Service Commissioner Stephen Sedgwick.
Some public servants earn tens of thousands of dollars less than colleagues in other agencies even though they are employed at the same level.
The pay gap that a typical Canberra bureaucrat faces could stretch to more than $47,000 a year by mid-2014.
An analysis of 103 government wage deals suggests salary differences across the Australian Public Service are rendering its job classification system redundant.
The wage data shows that many workers who accepted a promotion to another agency would end up copping a pay cut rather than a raise.
For executive level 1 jobs, which are the most common in Canberra, entry-level pay ranges from $89,796 (the Australian National Maritime Museum) to $115,751 (the Australian Office of Financial Management) – a difference of $25,955.
The gap between maximum salaries is wider still, with EL1 officers earning up to $47,658 a year more or less than other staff at the same level.
However, even at junior levels, such as APS1, base pay can differ by as much as $12,648 a year – about a third of these officers' entire salary.
Among larger workplaces, the Treasury and the Education Department are generally high-paying employers, while the Resources Department and the Bureau of Statistics pay comparatively little.
Public service wages were decentralised in 1997, allowing agencies to negotiate their own pay deals.
However, the Ahead of the Game report warned in 2010 that salary gaps between workplaces were discouraging public servants from changing jobs and gaining broader experience.
Public Service Commissioner Stephen Sedgwick told Fairfax Media it was important to give agency heads some flexibility to negotiate their own productivity and pay agreements with staff.
"None of us want to go back to a world that is so rigid that an agency can't pursue the agenda that it needs to pursue in order to achieve its objectives," Mr Sedgwick said.
"The government, in the last bargaining round, informed partly by the [Ahead of the Game] blueprint, had formed the view that we'd gone too far, that the pay disparities ostensibly for the same kind of work were too large."
The government used the last round of pay negotiations to ensure that most agencies' agreements ended on the same date – June 30, 2014 – and to prevent wage inequality from worsening.
Mr Sedgwick said the government "appears to have some appetite to continue that" but it was up to whoever was in office after the election.
"I think having a framework that encourages mobility within the service is a good thing. These things are always a question of degree."
The Minister for the Public Service, Mark Dreyfus, said he would not comment on matters before cabinet.
But he noted the government had begun to address pay disparity, and he would "like to build on this success in the next round of bargaining".
The Community and Public Sector Union says centralising pay negotiations would help prevent wage disparities.
However, its national secretary, Nadine Flood, said its first priority was preventing job losses.
"Reducing pay gaps is an important issue but the issues that are keeping public servants awake at night are job security and . . . conditions if there is a change of government."
She said centralised negotiations would help resolve common problems across the bureaucracy.
"Our policy position is not to have a single agreement, it hasn't been for years. Our policy position is that we want central negotiations with government on service-wide issues and their service-wide position and then you resolve the rest with each individual agency."