The head of the Department of the Prime Minister and Cabinet, Martin Parkinson, says Fairfax Media columnist Jenna Price's accusations this week are wrong and offensive.

Price wrote that women's policy under the Turnbull government "seems to be in chaos" and highlighted the lack of pay equity in Dr Parkinson's department.

She noted that executive level 1 officers in the department's office for women were paid significantly less – about $10,000 at the highest pay point – than EL1s in PM&C's social policy division.

Labor's spokeswoman for women's affairs, Tanya Plibersek, also told Price: "The fact [Prime Minister] Malcolm Turnbull is happy to tolerate such a significant gender pay gap in his own department, really says it all. He should be helping to close the gender pay gap, not contributing to the problem."

Dr Parkinson acknowledged the pay gap in his department, but said it had nothing to do with gender. Instead, it related to "the reality that the Australian Public Service does not have a single employment agreement".

He pointed out the pay gap was created before the last election – when he was still the Treasury head – when parts of the former Department of Families, Housing, Community Services and Indigenous Affairs were merged with PM&C.

"Until enterprise agreement negotiations are complete, all jobs in the office for women continue to be covered by the FaHCSIA enterprise agreement, while positions in PM&C's social policy division are covered by the PM&C enterprise agreement," Dr Parkinson said.

The PM&C secretary is one of few senior public servants who was appointed a "male champion of change", partly because of his efforts to promote female executives at the Treasury.

He said that, as someone committed to gender equality, he found Price's accusations "deeply offensive".

"I am committed to equal pay for equal work and am working to find a solution to the current enterprise agreement situation. In the meantime, within the parameters of their enterprise agreement, employees have the ability to negotiate a salary based on their skills and experience.

"To suggest my department is unfairly treating current and potential female employees is just plain wrong."

Price had also questioned why the office for women's new head, experienced public servant and consultant Amanda McIntyre, lacked "long-term expertise in women's policy".

However, Dr Parkinson strongly defended the appointment.

"Criticism of someone for their experience rather than their transferable skills and potential is one of the reasons that women do not progress at the same rates as men," he said.

"I am proud to have appointed an executive with significant runs on the board and potential to this key leadership role."

Dr Parkinson also noted he had elevated the office to a standalone division and appointed "one of my best operators to lead it".