The environmental group is concerned the developers are removing large boulders from an area where the penguins nest.
However, Kennedy Pt Marina Development Ltd said there had been a careful and temporary movement of some rocks.
"Ultimately we're objecting to the way that the Wildlife Act is applied in New Zealand," Forest & Bird chief executive Nicola Toki said.
"But in this instance we're objecting to the disturbance, because the Wildlife Act protects kororā or blue penguins and all of our special native wildlife from disturbance ... it means activity that could cause significant harm."
Toki said the legislation itself was well overdue for reform, and was heartened that Conservation Minister Kiritapu Allan had last year announced a review.
"The Wildlife Act is almost 70 years old and so as we learn more and more about what's going on for our endemic and special native species, something that came about in 1953 is no longer fit for purpose."