Rates are based on valuations made every three years, but can be changed earlier if improvements are made, Thornton said.
The property, which includes a tennis court, indoor and outdoor pools, and 12-car garage, was partly financed by former Hanover Finance director Mark Hotchin.
It was subject to a High Court asset preservation order stemming from legal action by the Financial Markets Authority in regard to the failure of Hanover.
Auckland Council member Cameron Brewer, who discovered the rates discrepancy, said it was unfair on other property owners whose places were not worth $39m, but were having to pay comparable rates.
"People will be disappointed to learn that New Zealand's most expensive home is paying rates according to a well out-of-date valuation when the place was a bomb site.
"This will really annoy many Auckland homeowners who have had their properties revalued by the council just days after completing renovations and, accordingly, their rates bill has been swiftly adjusted."
The construction project had famously dragged its feet, but should have been revalued in the interim, Brewer said.
"I believe it was sufficiently complete by mid-2013 to justify a revaluation and a recalculation of its rates but unfortunately council officers have decided to sit back and wait for the last picture to be hung before re-assessing its value."
Auckland Council spokesman Nigel Horrocks said council staff who knew about the situation could not be contacted because of the holiday break.
Brewer said council staff told him the mansion would be revalued in the next five months and the valuation would be used to set the 2014/15 rates.
Thornton said the discrepancy was "just another example of the unfairness of the system. A lot of the [property rating system] is just luck of the draw. If someone in that area is not paying their share, the rest of the city has to make it up."
