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Dunedin residents will continue to be vulnerable during extreme weather until there is a better understanding of the city's flood risk, an independent audit has found.

An audit of the city's stormwater network and flood risk by the Office of the Auditor-General found significant gaps in the Dunedin City Council's knowledge of its own network but did also find improvements.

The audit investigated how the council managed its stormwater system to protect people and their properties from the effects of flooding.

Two other councils - the Porirua City Council and Thames-Coromandel District Council - were also included in the audit.

The three councils were chosen as they cover different locations and have different ways of managing stormwater systems.

Each had an incomplete understanding of the flood risks in their areas, leaving communities vulnerable to unanticipated floods, the audit found.

While improvements were being made across each district all councils had more to do.

The audit found the Dunedin council did not know the condition of about 90% of its network, putting it at risk of making poor long-term decisions on how to manage the stormwater system.

Minimal information on the city's water courses and private drains meant there was a lack of clarity about who was responsible for water courses.

A lack of renewals and maintenance of those water courses and private drains could increase the risk of flooding.

Improvements were being made in all areas of the city's stormwater network and the council was proactive in clearing out stormwater systems before predicted extreme rainfall events, decreasing the likelihood of flooding, the audit found.

More money was also being spent on new infrastructure and renewals but the council first needed to catch up on a backlog of assets needing to be replaced because they were past their useful lives.

Council 3 waters group manager Tom Dyer said the report confirmed what the council already knew about the city's stormwater network and work to substantially improve it had started.

A significant body of work was already under way to improve the key areas highlighted in the audit but it would take some time to get to the position the council wanted to be in, Mr Dyer said.

The audit was a snapshot in time and a report in 12 months' time would find the council had a much better understanding of what needed to be done, he said.

"We want to take the time to do this work properly and it will be a core focus for the organisation over the next two to three years."

Auditor-general John Ryan said all councils needed thorough and reliable information about their stormwater systems and flood risks.

Councils needed to start making deliberate choices about their levels of service to protect communities from the risks associated with climate change and increased flooding events, he said.

A full copy of the report can be found on the Office of the Auditor-general's website.