Some properties north of Wangoom Road will come under flood controls for the first time with the proposed changes to the planning scheme - a move which attracted 21 submissions from concerned residents.

However, a "significant" area of land and properties will be removed from the flood controls under the proposed amendment.

An independent planning panel looks set to consider the rejigging of flood controls after councillors voted to refer the matter to the state government at their meeting on Monday.

Mayor Richard Ziegeler said it was an important piece of legislation because it affected so many people's homes. "We have to get it right," he said.

Cr Debbie Arnott said the plan would have "far reaching effects" on a lot of residents.

The proposed changes, based on computer modelling, attracted 21 submissions from property owners who were concerned about how it would impact their properties and hip pocket.

One submission said placing flood overlays on properties could lower property values and impact their ability to sub-divide or extend existing dwellings.

They also raised concerns there would be an "excessive increase in insurance premiums and even possibly not being able to insure properties due to the proposed flood overlay".

However, the council said previous planning panels had ruled the potential impact on insurance premiums was not a matter that should have bearing on the application of flood controls.

Another resident suggested flooding in their area was "entirely brought about" by a previous council installing "inadequate" culverts under Wangoom Road.

Others wanted the council to carry out more mitigation works rather than be hit with flood overlays on their properties.

However, the council said flood mitigation works and improvements across Warrnambool's catchment area would "cost the community millions" and could only be done incrementally over many years.

Property owners also took issue with what they say was "inaccurate modelling" but the council says it was best practice and computer modelling was the only practical method to reliably map the extent of changes to the flood shape across the municipality.

The council said it had checked the modelling where the accuracy had been questioned.

The amendment to the planning scheme aims to update flood controls on properties within parts of the Merri River and Russells Creek in north Warrnambool, and is part of what the council had called a "significant correction".

"There are significant areas of land currently covered by a flood control that will have that control removed through the amendment," the council said.

Cr Ben Blain said it was important the submissions were heard because it was a big change for the flooding scheme throughout Warrnambool.

He said it needed to go to an independent panel for "another set of eyes" on the issues.

"There are a range of very well-written submissions here and concerns from residents on this flood plain amendment," Cr Blain said.

"It think it's important they have their voices heard.

"This is an old overlay but a lot has changed in our city especially when it comes to infrastructure and mitigation measures that have been introduced.

"It think it is important to get this right now because it will have impacts on so many residents around Warrnambool."

Cr Angie Paspaliaris said the flood controls dated back to 1997 and the update would mean some properties would have flood controls removed, and others would have them added for the first time.

She said she hoped that by going to the independent panel it would lead to a fair and equitable outcome.

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