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Christchurch City Council head of parks Andrew Rutledge said it was contacted by a member of the public in November 2019 about the pontoons and the council has been working to find a permanent solution for their disposal.
Polystyrene from the damaged pontoons has been breaking down and polluting the environment since the pontoons landed at the site during a storm in 2000.
A contractor began removing the pontoons on Monday, with work expected to take three months depending on the weather.
Rutledge said a cost-effective way to remove the pontoons was found.
"We’ve worked with Lyttelton Port Company to contain the secure the pontoons until a suitable option for removal was found.
"Taking the pontoons away will improve the overall look of the area.
"It’s also good news for the Lyttelton community as part of our bigger plan for Naval Point, which is a significant marine and recreational asset that we want to improve."
The pontoons are made of polystyrene, wood and steel encased in concrete. They came from the Magazine Bay Marina, which was damaged by a storm in 2000.
Rutledge said once they are removed the pontoons will be moved to a covered facility and broken down in a controlled way into four different waste types. Three of the pontoons' components are able to be recycled, with the remaining 10 per cent going to landfill.
The council is also working on the Naval Point Development Plan, which is expected to go out for public consultation later this year.