The committee said it wasn't satisfied that negative effects could be avoided, remedied or mitigated. It also said it was concerned at a "lack of clarity" about the project's wider economic benefits, outside of royalties and taxes.
The company now has 15 days to lodge an appeal with the High Court.
In a statement, Trans-Tasman Resources chief executive Tim Crossley said the company was extremely disappointed with the decision.
"We have put a significant amount of time and effort into developing this project including consulting with iwi and local communities and undertaking detailed scientific research to assess environmental impacts of the project," he said.
"Our objective has been to develop an iron sands extraction project which achieves substantial economic development while protecting the environment."
The company, which has already spent more than $50 million on the project, will take the next few days to consider next steps. Crossley said staff and consultants in New Zealand now have a "very uncertain future" and that the local community would miss out on hundreds of new jobs and growth in GDP.
Kiwis Against Seabed Mining spokesperson Phil McCabe, who helped organise opposition to the project based on environmental concerns, said he'd thought the decision could go either way and was "stoked" at the result.
"It's a community victory," he said. "When you do feel passionately about something and you do stand up, it can make a difference."
He said the decision would set a new bar for the level of information required to support seabed mining applications.
The EPA is also considering an application by Chatham Rock Phosphate to mine phosphate nodules in a large area of seabed about 450 km east of Christchurch. Public submissions close on July 10 2014.
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