The EPA also said the company's proposal was "premature" and that it should have done further work on understanding the environment and engaging with local residents.
Trans Tasman now believes it has addressed those gaps.
Executive chairman Alan Eggers said the company had carried out additional research to refine the environmental aspects of its application, and had met with "a wide range of stakeholders".
The group travelling to Parliament tomorrow believes little has changed.
Kiwis Against Seabed Mining spokesman Phil McCabe said the method of mining was still experimental and damaging.
"It's inherently a destructive activity. If you're looking at deep-sea oil, you're poking a needle through the bottom of the ocean.
"But in this one, the moment they start, they're breaking stuff. There's sensitive habitats out there."
It was frustrating and exhausting to have to fight the company a second time, McCabe said.
Hikoi leader Debbie Ngawera-Packer said her iwi and residents of Patea, near the proposed mining site, did did not protest lightly.
"This is a real humble community that doesn't mobilise like that.
"They live off an average of $17,000 a year. They are used to going without and things not going their way.
"So when they mobilise it's because they feel there's a real injustice."
Trans Tasman is seeking approval to extract 50 million tonnes of seabed material a year, of which 45 million tonnes would be returned after the iron ore was extracted.
It estimates that the mining project would boost export earnings by $300m a year and would support up to 1650 jobs - 300 in the immediate region.