Warrnambool City councillors were deadlocked three-all when it came to a vote on whether man's best friend should be allowed on a section of the new trail that follows an old rail route around the western edge of Lake Pertobe towards the city.

Dog owners had lobbied for part of the route to remain accessible for walking their leashed pets, but Lake Pertobe staff and the council's environmental officer had pushed for a ban to protect abundant wildlife in the reserve.

Mayor Michael Neoh exercised his casting vote after arguing that the old rail branch line, which once served the former woollen mill and port, formed the boundary of Lake Pertobe.

"All it takes is one person to let a dog off a leash and attack a child or wildlife," Cr Neoh said during the vigorous debate.

"I'm not prepared to risk that."

He was supported by councillors Rob Askew and Andrew Fawcett, but councillors Jennifer Lowe, Jacinta Ermacora and Peter Hulin argued the ban was illogical and unnecessary.

The decision means anyone walking on the rail trail towards the city with a dog will have to detour through the woollen mill housing subdivision and use the footpath network.

Several dog owners told The Standard they had lobbied against the ruling because it stopped them from going the shortest way from the Harris Street dog exercise area towards the foreshore.

Cr Ermacora said the council should provide a better alternative route from Merri Street to the trail.

"It's an illogical scenario," she said.

"I agree Lake Pertobe wildlife should be protected, but this route is illogical."

Cr Hulin said the ban did not make sense considering the council's promotion of healthy lifestyle and walking routes. "We are not talking about the playground area," he said.

"We are talking about a wide path around the back of the lake where people should be able to walk their dogs on a leash."

Cr Lowe said all the community feedback to her supported dogs being allowed on the route.

"Dogs are man's best friend," she said.

"Surely it doesn't make sense to have the entrance to the rail trail with no dogs allowed."

Warrnambool resident Kim Wood said she regularly walked her dog near Harris Street and used to enjoy being able to use the old rail route to go to the foreshore.

"They seem to be regulating dogs out of Warrnambool, especially for those people who can't travel to the outlying areas," she said.