The federal environment department’s handling of major project approvals has been condemned in a scathing report by the auditor-general.

The auditor put referrals, assessments and approvals of “controlled actions”, such as mines, farms and tourism developments, under the microscope, when releasing a report on Thursday.

Problems were identified with not only the length of time it took to make decisions, but also the quality of the final decisions in terms of protecting national and world heritage sites, marine areas and water resources.

“The department has not implemented sound governance arrangements to support its administration of referrals, assessments and approvals of controlled actions,” the report says.

The auditor found the average overrun of timeframes for approval decisions was 116 days in 2018-19, with 79 per cent of approvals containing “conditions that were non-compliant with procedural guidance or contained clerical or administrative errors”.

“The department is unable to demonstrate that conditions of approval are appropriate,” the report says.

The implementation of conditions is not assessed with rigour.’’

In addition, the measurement of how well environmental protection laws were working was limited by the “the absence of effective monitoring, reporting and evaluation arrangements”.

The problems have already been acknowledged by the Morrison government.

The Environment Protection and Biodiversity Conservation Act is currently being reviewed by former consumer watchdog Graeme Samuel.

Environment department boss Andrew Metcalfe said in response to the report the EPBC Act is “complex and difficult to administer, and many of the decisions made are contested”.

In the short term, the department will take on board all of the auditor-general’s findings, but more reform would be needed after that, Mr Metcalfe said.

“It is anticipated the (Samuel) review recommendations will result in significant changes to the EPBC Act,” he added.

Tweet from @sarahinthesen8

Some of the anticipated changes will be in the areas of governance and risk management in administering referrals, assessments and approvals.

In recent months, the department has made some headway in so-called “congestion busting”, backed by a $25 million funding injection.

In the first quarter of 2020, the department met statutory timeframes for key decisions in 87 per cent of cases – up from 19 per cent in the final quarter of 2019.

And the backlog of overdue project assessments has been reduced by 43 per cent since December 2019.

The Wilderness Society’s Suzanne Milthorpe said the report was “utterly damning” and the solution was not to fast-track checks and balances.

“It shows that even when the department is aware of high risks of environmental wrongdoing, like with deforestation from agricultural expansion, they are unwilling to act,” she told AAP.

“The only credible response is to establish a well-resourced and independent Environment Protection Agency.”

-AAP