An independent $500,000 audit of the City of Perth's operations has identified a plethora of problems, including weak corporate business controls and inconsistent management reporting.

The report by Deloitte also raises concerns the council's rate of revenue growth is not keeping pace with expenditure growth, placing its operating surplus under unprecedented pressure.

When the audit was announced, embattled Lord Mayor Lisa Scaffidi denied it was in response to Premier Mark McGowan's threat to sack the council.

Since then, the State Administrative Tribunal ruled Cr Scaffidi committed 45 serious breaches of the Local Government Act by accepting gifts and travel, including a $US36,826 trip to the 2008 Beijing Olympics, funded by BHP Billiton.

Both Mr McGowan and Opposition Leader Mike Nahan called for her to resign in the wake of the findings but she has remained defiant.

The audit report, which has 17 findings, was commissioned by the City of Perth.

It focused on key areas including whether the organisation was complying with relevant legislation and the extent to which its decision making, controls and risk management were rigorous and transparent.

The report released today, reveals the council does not have a business plan for its parking business, which is a requirement under the Local Government Act for major trading undertakings.

One of the major findings was that management reporting was inconsistent and did not provide the executive leadership with the information needed to make effective decisions.

It also found there was an increased reliance on manual effort to maintain compliance and manage risk because certain business controls were weak.

The report says new roles and responsibilities, rolled out as part of an organisational restructure, were not well understood across the organisation.

"The lack of organisation-wide clarity and shared understanding of roles and responsibilities is causing indecisiveness, wasted effort and unconstructive tension between teams," the report said.

"Siloes are deepening due to ineffective team collaboration, which left unchecked may impact staff morale and retention of talent."