Andrew Podger says past governments went too far in giving agencies too much power to set their own pay rates, resulting in lasting damage to the Australian Public Service that will take some time to undo.

Mr Podger, public service commissioner from 2002 to 2004, says wages for public servants doing the same jobs varied widely across departments, a situation that undermined APS unity and bred resentment.

The former commissioner, now an Australian National University academic, made his criticisms of the system in a submission to the Senate committee that is to investigate the public service industrial disputes that are now into their third year.

By contrast, the current Commissioner John Lloyd says in his submission to the inquiry that APS wages and conditions are generous and the nation cannot afford any "enhancements".

Mr Lloyd has told the committee that the disputes have been fuelled by union behaviour rather than the Coalition's controversial public sector bargaining framework, which he says is "reasonable".

In his submission, Mr Podger says wage policymaking is still influenced by the ideas of the "New Management" in vogue in the early 1990s and its preoccupations with competition and productivity that are not compatible with public sector environments.

"In the public sector, treating each agency as a separate enterprise and limiting pay increases to productivity within each one, is doubly inappropriate if pursued other than on an occasional or short-term basis," Mr Podger wrote.

"Thirty years on, the case for this approach has long disappeared."

Mr Podger argues the devolved approach has led to unjust outcomes for public servants and done nothing for the much-vaunted goal of productivity.

"Pay for the same work and the same skills and experience now varies very considerably across the APS," Mr Podger says. "Far from promoting productivity, these outcomes run the risk of damaging morale and teamwork, and building resentment.

"Pay differences are not seen to reflect genuine merit, or genuine differences in skill sets or experience, but favouritism."

But in his submission to the Senate committee Mr Lloyd signalled his intention to keep up his push for productivity and said APS wages and conditions were "generous".

"Public service employment conditions are generous. In the current fiscal environment, enhancing conditions would place further pressure on agency budgets," Mr Lloyd wrote. "This would not be defensible to the Australian taxpayer.

"For this reason, the Workplace Bargaining Policy 2015 does not allow existing employment conditions to be enhanced."

The Commissioner's submission laid much of the blame for some of the most serious workplace disputes seen in the public service history on trade unions.

"The bargaining policy does not require the removal or reduction of existing conditions of employment," Mr Lloyd wrote.

"Conditions such as annual leave, personal/carer's leave, maternity and parental leave, employer superannuation contributions and redundancy provisions are protected.

"Union campaigns against new agreements have conflated the removal of restrictive work practices and union privileges with the removal of employment conditions."