The environmental regulator has been questioned why it is using the speed at which it issues environmental approvals to measure its effectiveness at protecting public health and the environment.

Between the lines of the department's 2015-16 annual report lies a simmering disagreement between the public sector watchdog, auditor-general Colin Murphy, and the director-general of the Department of Environmental Regulation, Jason Banks.

Mr Murphy has taken the Department of Environment Regulation (DER) to task for choosing to monitor how effectively it fulfils one of its key roles — ensuring pollution and land clearing do not put the health of Western Australians or their environment at risk — by measuring how quickly it finalises environmental approvals, permits and investigations.

But Mr Banks has responded by saying speedy approvals were a key part of being an efficient environmental regulator.

While the disagreement is being played out in the most bureaucratic of language in a document which is likely to gather dust on departmental shelves, it is an interesting insight into how policy debates are conducted among public servants.

For example, Mr Murphy chose to issue a qualified opinion on the department's annual report, a serious matter in the world of auditing.

He was critical of how the department used four KPIs which focused on the timeliness of regulatory activities — including the percentage of major resource projects work approvals decided within 60 days — to measure how it was avoiding risks to public health and the environment.

He called the KPIs to assess its effectiveness as a regulator "not relevant".

Environmental pollution breaches not reported

The average person may not see these as fighting words, but they prompted a three-page response from Mr Banks in the annual report, in which he strongly disagreed with Mr Murphy's criticism.

"The timeliness of regulatory decision-making for environmental approvals is central to the effective regulation," he wrote.

"Timeliness in decision-making is also relevant and of interest to Parliament, Government, industry and the community.

"Protracted regulatory decision-making can result in industry incurring unnecessary costs and may result in increased community concern due to extended uncertainty."

Mr Banks explained in the report that, after discussion with Mr Murphy, he agreed to introduce a new KPI but was informed by the Department of Treasury that it could not be used in this annual report.

While the nature of this new KPI is unknown, this year's annual report marked the first time the department has not published KPIs which show how many times environmental pollution exceeded safe guidelines.

It has prompted Greens MP Lynn Maclaren to call on the WA Government to reinstate vigorous environmental health and air quality measuring in the annual report.

Ms Maclaren said she agreed with the auditor-general, who had raised a serious issue with a department which she claimed was shifting its focus away from ensuring a healthy environment and towards speedy development approvals.

"Who else is going to challenge the director-general in this way?" she said.

"It shows that he is taking his job very seriously."