The court ruling says that under the EEZ Act, which took effect in June, the EPA can notify a marine consent application for public submissions and may hold a hearing.
But Anadarko did not need a marine consent because it already held a drilling permit, granted under previous legislation.
And the Environmental Defence Society says the opportunity for public and independent expert input will disappear under draft regulations to accompany the new act.
The proposed regulations, out for public comment until January 31, would make offshore exploration drilling a non-notified activity.
EDS chairman Gary Taylor - who first raised concerns that the EPA had not seen Anadarko's emergency response plan before approving its impact assessment - said the court ruling sets a low threshold for offshore drilling applications. He believed there were grounds for appeal.
"This is not what the act requires or what the public wants."
Greenpeace chief policy adviser Nathan Argent said the judgment showed the EPA could approve offshore drilling without looking at documentation on responses to the environmental effects of a disaster.
While a loss of well control was highly unlikely, the risks were higher in deep water and the environmental effects could be catastrophic.
But EPA chief executive Rob Forlong said the new regulations would enable the authority to take into account information from other sources when they became fully effective in June.
Anadarko began drilling off Raglan last month.