Images of the damage posted online show the John Howard statue graffitied with the word “homophobe” in red paint.
On the statue of Tony Abbott is the words including “pig”.
City of Ballarat councillor Amy Johnson took to social media to express her concern. She said the statues cost between $30,000 and $60,000 to produce.
“Any normal person would be disgusted at the mindless vandalism of the statues in our Botanical Gardens last night,” Cr Johnson wrote.
“Our Prime Minister’s Avenue is an integral part of the garden’s precinct, which attracts thousands of tourists to Ballarat every year.
“The right to publicly demonstrate is one most of us respect. That right does not extend to wanton vandalism.”
The vandalism follows the defacing of a statue of Captain James Stirling in Perth’s central business district on Friday.
The statue had its neck and hands sprayed red and an Aboriginal flag painted over the inscription a day before a planned protest was due to run.
In London, a statue of Winston Churchill has been sealed inside a steel barrier as fears grow it may be torn down or become a flashpoint for clashes between rival protesters this weekend.
It is not the first time statues honouring leaders have been damaged in Victoria. In January 2018 a James Cook statue in Catani Gardens at St Kilda was defaced with graffiti as well as those paying tribute to explorers Burke and Wills in Melbourne CBD as Victorians prepared to mark Australia Day.
Years earlier Cooks Cottage at Fitzroy Gardens was vandalised with anti-Australia Day celebration tags.
Anyone with information on the Ballarat graffiti is urged to call Crime Stoppers on 1800 333 000.
Erin covers crime for The Age. Most recently she was a police reporter at the Geelong Advertiser.