Forest & Bird took the case against the council as part of a campaign to get pockets of native bush included in the district plan.
Its lawyer, Peter Anderson, said those areas had little protection.
"There's between 326 and 361 significant sites in New Plymouth district which have no protection under the plan, and they are at risk from clearance - they can be cleared without resource consent and we think that is a significant risk."
Many of the significant natural areas were home to threatened plants and animals, he said.
The council's group manager strategy, Liam Hodgetts, said it had in the past preferred to work collaboratively with landowners.
However, he said the areas would now be included in the district plan as part of the current review process.