The building is the site of the proposed Bridgewater Quay project.
The fire was contained within an hour of Fire and Emergency turning up.
"We're unsure of the cause, we don't think it's suspicious but a fire investigator will help determine that," Whanganui area commander Gary Ward said.
"The crews have worked really well, especially the first team in because the fire was unvented so potentially dangerous for the crews and building, but they managed to cut it off."
The fire was contained to the first floor in a workshop area of the building.
Ward said there isn't thought to be any damage to other parts of the building.
Bridgewater Quay developer John Hay recently lodged resource consent with council to refurbish the building into 20 apartments.
Hay said the fire isn't likely to create too many issues for the development moving forward.
"The engineer will have a look and make sure nothing has happened to the structural integrity of the building but it's just an inconvenience more than anything.
"Building developments take a while to come along and this is just another twist in the road, it's just fortunate no one was hurt and the fire service did a great job."