Amphipods are normally up to three centimetres (around an inch) long and the University of Aberdeen's Alan Jamieson said he was stunned to find the 28 centimetre (11 inch) giant when emptying traps on his research vessel's deck.
"I stopped and thought 'what on earth is that?' whilst catching a glimpse of an amphipod far bigger than I ever thought possible," he said.
"It just goes to show that the more you look, the more you find," NIWA principal scientist Ashley Rowden said.
"For such a large and conspicuous animal to go unnoticed for so long is just testament to how little we know about life in New Zealand's most deep and unique habitat."
Supergiant amphipods have been found only once before, in the 1980s. But that was off Hawaii, about 7,000 kilometres (4,500 miles) to the north, and NIWA said it was yet to determine if the latest catch was a new species.
Scientists said they did not know why the deep-sea creatures evolved to such a huge size.
(c) 2012 AFP