"At this point, our priority is to protect the river from any contamination and ensure the safety of workers and the community."
The announcement of the demolition comes ahead Tuesday's public hui on Te Pūwaha, including the reveal of plans for the North Mole revamp and a full plan for the future of Whanganui's port.
People can visit the Duncan Pavilion between 9am and 5.30pm before short presentations between 5.30pm to 6pm.
The significant subsidence under the wharves, including the Victory Shed, has been of concern to the council for a number of years.
Whanganui mayor Hamish McDouall, a member of the governance group for Te Pūwaha, said the Victory Shed was built after World War II to support industry and commerce at the port.
"According to records, it was originally named the 'Victory over Japan Shed' with the intention that it would become a practical and functional war memorial," he said.
McDouall said locals, particularly in Castlecliff, will have an association with the structure.
"Although the building is not heritage listed, we acknowledge its social and historic connection within the Te Pūwaha project."
Construction on the Whanganui wharf began in 1884 and included the Castlecliff railway station as a private venture launched by the Head family, then the Castlecliff Railway Company.
The area is a pre-1900 archaeological site and an archaeologist is working with the Te Pūwaha project.
As part of the wharf redevelopment, photographic records will be taken. Where possible, materials from the building will be salvaged and reused, including the barn-style doors and runners and the name from the side of the building.
This part of the Te Pūwaha project will upgrade 424m of the wharf area including 200m on Wharf 2 to enable the safe operation of commercial marine activities and 224m on Wharf 3.
The project will also include the development of marine infrastructure, provision of a hardstand and runway suitable for a 300-tonne vessel hoist to enable boats to be lifted in and out of the water, and improvements to silt remediation technology to enhance the local boat building and marine industry.