Non-toxic shot does not contain lead and the most commonly available type uses steel pellets.
The use of non-toxic shot for waterfowl hunting was already mandatory in many countries, including the United States, Canada, Europe and some Australian states.
"Lead shot will be progressively phased out from 2018 for waterfowl hunting over and around large bodies of water, so by the time the 2021 season begins, all hunters will be using non-toxic shot for this type of hunting," Fish and Game chief executive Bryce Johnson said.
The move completed a process which began nearly two decades ago.
"The original decision to phase out lead shot for waterfowl hunting was made in 2000 after the Government decided to adopt Australian and New Zealand guidelines for fresh and marine water quality which identified issues with lead," Johnson said.
"The problem is waterfowl get poisoned when they pick up fired lead shot and eat it as a grit substitute to help them digest their food."
New Zealand scientific studies showed the problem was the same here as overseas, he said.
Johnson said extending the non-toxic shot requirement to most shotguns was inevitable.
"At the moment, nine out of 10 of our hunting licence holders already use non-toxic shot because they own 10 or 12 gauge shotguns.
"Advances in ammunition manufacture means good quality non-toxic shot is now available for smaller shotguns, so we are asking the small minority left to follow their example.
"The only exemption will be for the small bore .410 shotguns which are sometimes used by beginner hunters and for which humane non-toxic shot loads are not available."
Barry said she fully supported the move.
"Lead is toxic - so much so that there is no level of exposure which is considered safe," she said.
"New Zealand has already banned its use in paint and petrol."
