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The multi-role HMNZS Canterbury's two landing craft will be replaced because of design flaws which make the bow ramps prone to cracking.
There are also problems loading cargo at sea, and stability issues.
The problems are the latest to affect the fleet of seven ships bought by the Government for $500 million.
Australian builders BAE Systems will pay $85 million, some of which will go towards designing and building two new landing craft medium (LCMs).