TTR had previously been declined consent in 2014, then granted it in August 2017 by a decision-making committee of the Environmental Protection Authority (EPA).
The consents would have allowed TTR to suck up 50 million tonnes of iron-sand a year from the seafloor 22-36km offshore, and export 5 million tonnes of iron ore to Asia.
The company said it would have created 300 jobs and increased New Zealand gross domestic product by $160 million.
The decision-making committee set 109 conditions for the mining. They included the company spending two years assessing the marine environment before it starts mining, and then assessing damage to sea life after five years.
If sediment affected the clarity of coastal water by more than 10 per cent, it would have to stop mining.
Justice Churchman said the conditions amounted to an adaptive management approach - one where conditions were set after the activity was tested.
Under exclusive economic zone (EEZ) legislation, residues from mining are classed as hazardous substances. An adaptive management approach cannot be taken to their discharge, Justice Churchman said.
The judgement also said the consenting authority must favour caution and environmental protection when information about the receiving environment is uncertain or inadequate.
He sent the matter back to the decision-making committee to consider in the light of his decision that it had used an adaptive management approach.
The consents were appealed to the High Court by seven groups, representing environmental, iwi and fishing interests.
Kiwis Against Seabed Mining chairwoman Cindy Baxter said her group made the adaptive management argument in the High Court.
Justice Churchman agreed with KASM's lawyers, but didn't agree with much else from the appellants, Baxter said.
High Court appeals must be on matters of law. He said the question of whether the committee had enough information to make a decision was a matter of fact, not law.
He was also unable to consider the fact the decision was made on the casting vote of chairman Alick Shaw. And he said TTR had taken reasonable steps to identify effects on iwi, despite the lack of a cultural impact assessment.
If such an assessment was mandatory then iwi would be able to block consent by refusing to take part.
He considered TTR has met its obligation to state the economic benefit from the mining, and that its $500 million public liability insurance was an acceptable alternative to a bond.
The appellants said modelling the effects of the mining was not good enough evidence - but he said modelling was the only alternative apart from actually doing the mining.
