Fish and Game New Zealand says Minister of Conservation Steve Chadwick has agreed to ban the use of felt-soled wading boots for freshwater fishing from 1 October.
Boots with felt or fibrous soles are popular with anglers because they provide a good grip on slippery rocks.
But Fish and Game chief executive Bryce Johnson says their use increases the risk of spreading the invasive alga didymo.
The alga was first found in a South Island river in 2004 and can be spread by a single drop of infected water.
Mr Johnson says anglers still need to check, clean and dry their fishing gear, and leave it at home if they are visiting the North island.