Warrnambool City Council will replace a small copse of Casuarina trees for several species of low-growing native shrubs, including the endemic Granny's Grave correa.

The strategic vegetation management project is aimed at restoring view across Lake Pertobe from Cannon Hill.

Warrnambool mayor Tony Herbert said the community had told the council it wanted the view of Lake Pertobe from Cannon Hill reinstated.

"This project will help ensure Cannon Hill continues to be the popular lookout point enjoyed by residents and by visitors to the city," he said.

"Over recent years there have been ongoing native plantings on Cannon Hill and we have also removed a number of Cypress trees to help maintain the view and to tip the balance towards native plants being the dominant vegetation type in the area.

"Council also operates a pest animal control program that tackles rabbits on Cannon Hill and elsewhere around the city."

The clearing and replanting is expected to take place in late June.

The area was beautified in 2016 with the removal of a self-sown pine tree and shrubs.

The works opened up the lookout to include a more expansive view of Lake Pertobe and Lady Bay.

The lopping of trees has proved controversial over the past year in the city with outcry from the public about the proposed axing of two Moreton Bay fig trees.

The trees were earmarked for removal because they were interfering with underground services.

The trees, on the corner of Raglan Parade and Banyan Street, were planned to be removed, however after strong support from the community to retain them, city councillors voted to keep the two large figs. A petition to keep the trees garnered more than 1500 signatures.

Warrnambool was originally protected by the cannons at Cannon Hill following the Crimean War. There was concerns Imperial Russia would attempt an invasion, so defences along the Victorian coastline were strengthened.