New evidence shows the deep sea coral forests home to orange roughy are failing to recover from trawling.
NIWA marine biologist David Bowden said that 15 years after being trawled, a seamount on the Chatham Rise showed no sign of recovery.
"It's a long term change that we are exerting on the ecosystem."
Orange roughy grow slowly and live to 150-years-old, and the fauna on the underwater volcanoes where they live and feed are similar.
"The ocean floor, the corals, the sponges that also takes centuries to recover," says Greenpeace director Russell Norman.
Nearly a kilometre deep, the Graveyard Knoll is a group of 28 seamounts on the Chatham Rise.
Of the six studied, Morgue has been closed to trawling since 2001. Graveyard has been trawled heavily, while others have never been trawled.
Scientists say the difference between trawled and untrawled seamounts is stark.
"The hills that have never been fished we see luxuriant coral reef growth - much of the seabed is covered by corals whereas on the fished seamounts we see most of the coral is removed," says Mr Bowden.
The deep sea fishing industry says the research will help them operate more sustainably.
Sealord Group operations general manager Doug Paulin, says humans need to change how they're using the ocean.
"Think about the time humans have been on the planet which is a relatively small amount of time, and those areas are closed to fishing - we've got millennia for those corals to recover."
But Mr Paulin says trawling is necessary.
"There are some species of fish where they swim very close to the bottom and unless you trawl on the bottom you're simply not going to catch them."
Mr Norman says fish like orange roughy should be considered a luxury, not a necessity.
"Bottom trawling should be banned, it's like destroying an ancient kauri forest in order to catch some kereru."
Government representatives from around the world are in the process of creating a legally-binding treaty to protect the high seas, those which are outside of any countries' jurisdiction.
Greenpeace hopes that will see the end of bottom trawling.