It disputed that swamp kauri "table-tops" without legs or with light surface carving could lawfully be exported.
But Justice Toogood ruled in the High Court at Auckland last year that ancient swamp kauri was not subject to the Protected Objects Act and its export could continue.
He said imposing extra restrictions would "create an oppressive regime restricting the removal from New Zealand, by ordinary travellers, of everyday products which have no
particular significance".
He also refuted the society's argument that buried swamp kauri was a fossil worthy of protection under the act, like kauri gum and scrimshaw whale bone.
Justice Toogood noted there had been historical concern around the export of kauri stumps but he was satisfied with MPI's system which he said had "progressively improved its procedures" since late 2011.