He said the national office reviewed the file given to them by Wairarapa SPCA, and spoke to those they felt necessary to speak to - including the owner who was very "co-operative".
He said the file was presented very late in the investigation and there wasn't "anywhere near" enough evidence to prosecute.
Council group manager planning and environment Glenn Bunny said he first heard about the decision not to prosecute the owner after being approached by media.
Mr Bunny said he and three staff had visited the site and he had expected to have been spoken to.
"It's the SPCA's decision and their mandate to prosecute or not."
Wairarapa SPCA manager Val Ball did not want to comment.