It is the successor to Aquos Yachts' $58 million 45m craft Big Fish.
Star Fish was due to be delivered to its owners in March next year.
McMullen & Wing co-managing director David Porter said an "incredible amount" of work had gone into the vessel's construction and much of the furniture and fittings were in place.
"I'm gutted, quite frankly, and I'm gutted for our staff because it's going to have a huge impact on them. Some of my team are in tears."
It was yet to be determined whether the vessel could be salvaged, he said.
"We'll see what happens and we may well complete it, who knows, but there's a lot of work to do now.
"I think, best way described, it has suffered substantial damage."
Star Fish would have been the largest vessel built by the company, and one of the biggest superyachts built in New Zealand.
"By world standards it's up there," Mr Porter said.
Aquos Yachts could not be reached for comment.
Up to 90 firefighters and 20 fire trucks were involved in putting out the huge blaze.
Auckland central area commander Kerry Gregory said once the burning building was dealt with, firefighters still had to get to the flames inside the vessel's hull.
"It's a fire within a fire so really access is a big problem for us. In confined spaces there's a real build-up of heat so we've got to make sure it's safe for our firefighters to get in there.
"It's a hard job so there's lots of rotating of crews because they just come out exhausted."
Fire safety officer Phil Faidley said the investigation into what caused the blaze would probably take several days to complete.
