He said the plan would result in a huge rate increase for the mall's 126 tenants.
Mr Lynch said the capital value system targeted quality capital-intensive developments such as shopping centres unfairly.
Shopping centres paid for their own parking yet retailers on the main street, where parking was provides by the council, stood to gain.
Mr Lynch urged the council to focus on changing its district plan to control development rather than boosting Hamilton's CBD at the cost of other long-term investors.
He said the Australian shopping giant would "seriously consider" appealing the council's decision if it went through in its present form.
Waikato Property Council president Graham Dwyer supported a system under which the user paid for services received.
"It's illogical [that] rubbish or water relates to capital or land value. It relates to rubbish bags ..."