Protesters have gathered around a marina construction site on Waiheke, where developers are removing rocks from part of a wall that kororā, or little blue penguins, live and nest in.
The group Protect Pūtiki has been trying to stop the Kennedy Point marina being built.
They fear it will harm the kororā population, so last year they spent weeks occupying the site.
This week DOC granted permission for the developers to handle the kororā and move them to safety.
Spokesperson for Protect Pūtiki and environmental group Mauri o te Moana, Bianca Ranson, said she is upset with what she had seen at the marina today.
"They've got a digger with a claw attachment, which is reaching down and it's grabbing on to the rocks, which as they move them, at times are slipping and dropping."
She was among 30 - 40 protesters that had gathered, despite blacked-out fences obscuring most of the site from view.
In a statement Kennedy Point Marina Director Kitt Littlejohn said there had been "careful and temporary" movement of rocks on a small section of the breakwater wall above the mid-tide line.
He said the Wildlife Act Authority granted by DOC ensured all the necessary protocols were in place so that the kororā were protected.
"The planned works affect a very small area of the rock breakwater wall at Kennedy Point - less than 5%. The works are also taking place outside of the breeding/moulting season when kororā are less vulnerable to disturbance and unlikely to be confined to their burrows."
If any kororā need to be moved, he said seabird ecologist Dr Leigh Bull would take them to a suitable release location further along the breakwater.
"She will be on-site at all times when the temporary rock disturbance works occur. The work will also be monitored by Department of Conservation staff and ecologists."
The rocks will be put back within a maximum of 6 weeks and the kororā habitat reinstated, he said.
Kennedy Point Marina said no kororā were handled or moved during today's works.
Earlier DOC had said that waiting for the birds to move posed a greater risk than handling them.
Kennedy Point Boatharbour Ltd, the firm constructing the marina, have said it will be built with minimal disruption to the sea bed and shoreline.
Their website said the work involved moving rocks from about five percent of the wall, for up to three weeks, before the rocks are put back.
Workers would follow a management plan designed to protect the kororā which had been approved by Auckland Council.
This included waiting until the nesting and moulting period finished, and checks that there are no kororā left in the area of the wall being worked on while the movements are underway.
"Additionally, the team has been working on a number of options to create predator-free penguin habitats on the perimeter of the Marina."