WA’s environment regulator says rapidly approving projects shows it is protecting the public.

But senior officials have questioned this line of logic, saying speed is not a good measure of effectiveness in safety.

The debate between director-general of the Department of Environmental Regulation, Jason Banks, and the public sector watchdog, auditor-general Colin Murphy, appears in the department's 2015-16 annual report.

One of the key roles of the Department of Environment Regulation (DER) is to ensure pollution and land clearing do not create risks to the health of Western Australians or their environment.

But Mr Murphy says the DER has been monitoring its effectiveness by measuring how quickly it finalises environmental approvals, permits and investigations.

Mr Murphy issued a qualified opinion on the department's annual report – which is a big deal in the auditing world.

He criticised four of the department’s KPIs - including its measurement of the percentage of major resource project approvals decided within 60 days.

He said these were not a gauge of how the DER is avoiding risks to public health and the environment, and so were “not relevant” to assess its effectiveness as a regulator.

Mr Murphy’s fighting words prompted a three-page response from Mr Banks in the annual report.

“The timeliness of regulatory decision-making for environmental approvals is central to the effective regulation,” the regulator 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.”

But the report also shows there has been some progress in the matter, with Mr Banks agreeing to introduce a new KPI.

The nature of this new KPI is unknown, as the Department of Treasury called for it t be kept out of this year's annual report.

The documents are also conspicuously missing KPIs for how many times environmental pollution exceeded safe guidelines, something it had until this year reported.

The state’s Greens say it is evidence that the DER is weakening itself, and called for more vigorous environmental health and air quality measuring to be reinstated.