The minister said the trust's case was "weak" because Maori had not fished at the islands for a decade.
Te Ohu Kaimoana spokesman Jamie Tuuta said iwi's recent absence from the fishery was irrelevant. Treaty of Waitangi rights were intergenerational and it was up to Maori to decide when it might fish there, he said.
A Treaty settlement signed in 1992 and known as the Sealord deal gives fishing rights to Maori, and requires the Crown to include iwi in statutory decisions. Mr Tuuta said Te Ohu Kaimoana was only told of the proposed sanctuary the night before it was announced in a high-profile event at the United Nations in New York in September.
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• Kermadec sanctuary to go ahead despite iwi opposition
He said legal action was a last resort but was necessary because iwi had been ignored.
"If the Government are looking to expropriate or impact on those rights, then the decent thing to do is to sit down and discuss those matters with iwi."
The Government consulted with northern iwi Ngati Kuri and Te Aupouri on the sanctuary and has allocated three places on a governance board for Maori. But iwi say this does not go far enough, because a total of 58 tribes had interests in the fishery.
It is the second time in a year that Dr Smith's policy has led to a legal challenge. In June, Ngati Whatua sought a judicial review of the minister's decision to offer surplus land in Auckland to developers without offering it to Maori first.
Dr Smith defended his record on Treaty issues.
"I do accept when Government tries to do things there will sometimes be a bumpy ride in accommodating Maori perspectives," he said.
"But it is just inevitable when a Government is ambitious and wants to get more houses built and wants to protect areas of ocean."
Around 20 tonnes of fish, mostly tuna, is caught within the boundaries of the proposed Kermadec Ocean Sanctuary each year. The fishing take is worth around $250,000 but iwi say it would be worth much more if fully developed.
The proposed sanctuary covers 15 per cent of New Zealand's exclusive economic zone and would include 39 species of sea birds, 35 species of whales and dolphins, three species of endangered turtles, and 150 species of fish.