He argued the ruling was "manifestly unjust and wrong in law."
Justice Andrews, in her written ruling, dismissed the application for judicial review.
Mr Mackenzie had not pointed to any particular alleged statutory duty by Crown Law, nor had he established any basis on which a claim for breach of duty of care could succeed, she said.
She also ruled that Associate Judge Bell had not erred in finding the Attorney General was the appropriate defendant, and the proceedings must be struck out because it was statute-barred.
Justice Andrews invited the Attorney-General to "consider the propriety" of not enforcing an order seeking payment of legal costs from Mr Mackenzie.
"I have no reason to doubt that Mr Mackenzie filed the proceedings genuinely believing that the taking of his son's heart, without consent, and seen by him as mutilation of this son's body, demanded redress in the form of an acknowledgement, an apology, and compensation."
Mr Mackenzie told the Bay of Plenty Times last night that he was "absolutely dumb-founded" by the ruling.
"I really can't believe it. I'm convinced I have a rock-solid case.
"Crown Law may think this is the end of the matter but I am to committed to seeing this through to the end," he said.
Timeline
October 2, 1987:
Kenneth Mackenzie's life support turned off.
March 21, 2005:
His father, John Mackenzie, is informed his son's heart was removed and transplanted into a 16-year-old.
November 24, 2006:
Damages sought from the now disestablished Crown Health Financial Agency. Claim denied.
November 23 , 2012:
Mr Mackenzie lodges a formal statement of claim against the agency but is repeatedly denied legal aid.
January 31, 2013:
Attorney-General files application to strike-out statement of claim.
February 17, 2015:
Associate High Court Judge Roger Bell strikes out Mr Mackenzie's claim.
July 31, 2015:
High Court Justice Pamela Andrews hears a judicial review application.
