It was applied to all commercially rated properties in an area within the boundaries of Nelson St, St Aubyn St, Hastings St and Southampton St East.
From next month, all of Mr Vogtherr's properties, which he had owned for almost 60 years, would receive a rates increase of more than $600, or a 38 per cent increase in total.
He said he had been a "good landlord" and managed to get all three properties leased, although one of his tenants would only accept a one-year lease and forced him to reduce the rent. His overall returns were "rather small".
"Our rates are already $5290, and now they want an extra $1800, for no good reason."
He believed his buildings, located on St Aubyn's St East, were a far cry from the city's inner retail area, and should not be included in the designated CBD. "I say we're not in the CBD, and we still are not."
His daughter, Claire Vogtherr, owner of the well-established Holly Bacon company on the corner of Warren St and St Aubyn St, had also seen a rates increase of more than $1000 per year as part of the change.
A Hastings District Council spokeswoman said the increase was the result of a correction to its rating database.
"After an audit of the properties within the targeted rating area in the CBD area, council officers wrote to 33 land owners of commercial properties and advised them that it planned to correct its rating database and apply the targeted rate to their properties."