Heritage consultant Dr Ann McEwan said the council's evaluation criteria meant the former Arthur Yates & Co office and warehouse between Albert, Wolfe and Federal Sts should be ranked A.
The buildings were intimately connected with a person of national importance - Arthur Yates, who turned Yates & Co into the largest seed company in the colonies, she said.
In a written decision from a panel headed by Justice Craig Thompson, the court ruled that an appraisal of the main building by the former Auckland City Council in 2005 as a category B building was "much more defensible".
Mr Matson, who has been fighting to save the buildings for eight years, was surprised the court had rejected the "unanimous position of five heritage experts" and had proceeded to score the building itself.
Mayor Len Brown was also disappointed that the court had reinforced the former Auckland City Council's category B rating. He said the ruling highlighted that going to court would not always succeed.