The other 44 light poles - of the total 225 planned under the project - are located in the Ballarat Botanic Gardens and received the go ahead in September last year.

The now approved permit was submitted to Heritage Victoria in April, receiving 109 submissions, one in support of the proposal and the remainder objecting to the proposal in some form.

Friday's outcome means the $2.5 million project can progress to next steps.

Prior to commencing work on the project, the City of Ballarat must submit a Construction Management Plan, construction-ready drawings, and a Tree Management and Protection Plan to Heritage Victoria for approval.

Scott Gallop of the 'Get our Lake Wendouree lighting right' group said he was disappointed in the decision, citing the lake ecosystem, light pollution and aesthetic of the lights as key concerns.

"How it affects the wildlife, the birds, the insects was never looked into, what effects it would have on the insect population around the lake, which obviously affects the fish and the whole ecocycle in that lake area," Mr Gallop said.

"We're not against the lights. We think there should be some type of lighting, such as in-ground lighting ... which just shines enough light for [runners] to run past and that way people can still see the track."

Documents released on Friday by Heritage Victoria stated the works would "not detrimentally affect the cultural heritage significance of the place" and "the lighting poles will improve the amenity and safety of recreational users of the lake".

The statement also notes physical impacts to existing trees will be mitigated in a number of ways, including through a Construction Management Plan and a requirement for hand boring.

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City of Ballarat mayor Cr Daniel Moloney said it would have been odd to have a different outcome for the remaining light poles than the September decision.

"It's unfortunate that it's been dragged out for an extra few months but ultimately, the decision makes sense," Cr Moloney said.

"This has been a long and thorough process that has gone through planning permits, heritage permits, several stages of consultation over several years, there's been different design, different designs of trial lights."

The lights will be time limited and painted green to help blend in the environment more.

"These are lights that are in hundreds of locations around Australia around lakes and waterways ... it's not like we walk around the gardens in Melbourne or the lakes in Bendigo and Shepparton and think about how devastated those locations are," Cr Moloney said.

"If anything, it's added a new lease of life and the opportunity for people to get greater enjoyment out of those wonderful places, and I'm sure we can achieve the same here in Ballarat."

Funding for the project was promised during the 2018 state election campaign, with the plan to improve safety for lake users backed by both major parties.

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