Marina Shum, owner of Seacrest Village Chinese Restaurant on Harman Road, said the clinic had been approved for the space between her restaurant and a fish and chip shop without any notice to the neighbouring tenants.
She said having a vet near food outlets was not suitable and she was concerned about hygiene.
"My customers are disappointed. Im worried the business might suffer," she said.
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READ NOWMs Shum took the matter to Hillarys MLA Rob Johnson, who wrote to Health Minister Kim Hames.
The Department of Health said it was a planning issue and the responsibility of the City of Joondalup.
At the August 17 council meeting, a 227-signature petition was presented to the City opposing the location of the vet clinic with concerns about health, hygiene, safety and noise.
Joondalup acting chief executive Mike Tidy said the City approved the land use change from shop to veterinary hospital " an allowed use in a commercial zone " on June 22 under delegated authority,
He said the use was considered to fully comply with the requirements of the planning scheme, there was sufficient car parking across the site to accommodate the development and no external changes to the building except signage were proposed.
"The applicant addressed any potential noise from barking dogs, advising that all animals were to be accommodated within the building and that the dog ward would have soundproof dry walling and solid brick walls," he said.
"The obligation of ensuring the provision of safe food and complying with relevant food safety related legislation will continue to rest with each individual food business in the shopping centre and a veterinary centre next to a food business does not impact on food safety risks."