Part of the fencing installed to keep kororā out has of the Shelly Bay development been tampered with after the developers blocked the area and several endangered penguins were photographed stranded on the road.
Recently, wire fencing was installed at the underskirts of the already-installed fencing around the development, which has begun construction.
The set up means penguins are immediately being met with the fence and remain on the road unless they turn around back to the shore side.
Roseneath resident Charlotte Daniels was driving past the controversial Shelly Bay development just before 9pm on Saturday when she saw three of the birds, also known as kororā, on the road.
She said it looked like they were trying to get home.
"There was one of them that was frantically looking around the fence, and two of them were kind of huddling around together," she said.
"I was a little bit worried about them getting hit by a car so I waved my arms and tried to shoo them back towards the water."
This morning, it appeared one part of the fencing had been tampered with and elevated enough to fit a penguin through.
Further down the site, contractors were installing their own orange mesh fencing to the underskirts of the buildings and fences.
Four nesting boxes have been installed at the front middle of the development, but is directly across from a slanted seawall at an angle penguins can not scale.
At a minimum, if kororā got up from a pre-existing staircase it still is about 60m to the nesting site.
North of the seawall and development is rocky terrain and where penguins have been sighted over the weekend stranded on the road in front of the barricades.
A section of the fence appears to have been raised at the north of the development - across from where the seawall ends and rocky terrain begins.
Wellington penguin expert Mike Rumble said penguins were creatures of habit, and wouldn't necessarily use any new nesting boxes.
"They will always attempt to go back to their original nesting site. They can't turn left and go to a new one just because they happen to see a box, they will still try and go back to where they were."
Nesting season in this part of New Zealand ran from mid-August to November/December, and nothing should prevent the at-risk kororā from returning to their nests during that time, he said.
"They're now in a position where they've got to wander around trying to find a new place to nest and whether they're going to actually find one is a $64 question because they don't know where to go, and so we could end up with a situation taken to the worst case picture where a nesting season is completely messed up."
Rumble said another concern was whether there were birds already nesting inside the fenced-off area.
He wanted to know whether a bird management plan was in place, and said work on the development should stop until the kororā were safely protected.
"There's a strong possibility in my mind that the bird management plan hasn't been yet approved but has been implemented in a rather haphazard way," he said.
"The last thing we want to do with all the hard work that's been going on is make life any more difficult for penguins than it already is thanks to human activity."
Predator Free Miramar founder Dan Henry said the fence was clearly designed to keep kororā safe from construction, and there was a gap to allow them to reach four new nesting boxes.
But he said the penguins were clearly confused.
"They want to head up the hill where they normally nest and not be ushered into social housing for penguins," Henry said.
"To me it's the first visible signs of exactly what happens when you try and put an intense development in an ecological greenspace."
This afternoon Wellington City Council staff had been taking a look at the fencing and the general area to see if any changes could be made to lessen the hazards and get the penguins off the road.
In the meantime, the council is warning drivers to take extra care on the Shelly Bay Road, especially at night when kororā do return to their nests or meet the fence.
Mau Whenua, a collective of Taranaki Whānui who occupied the site in opposition for development for 525 days, said they were "upset to see evidence of our taonga kororā displaced, confused and in danger as they go into nesting season at Marukaikuru/Shelly Bay."
"We were of the understanding that a requirement of consent was that there would be a robust, effective plan developed with kororā and relevant mātauranga Māori experts to ensure this exact situation was avoided" a statement from Mau Whenua read.
Taranaki Whānui ki Te Upoko o Te Ika, also known as the Port Nicholson Block Settlement Trust, has asked the community not to intervene with the site.
"Taranaki Whānui take seriously our responsibility as kaitiaki and are working with experts and stakeholders to protect our native wildlife at Shelly Bay Taikuru", chair Kara Puketapu-Dentice said.
The iwi said it had co-developed a kororā management plan alongside experts to ensure the birds protection. Experts were from Boffa Miskell, the Department of Conservation, Places for Penguins Wellington and Wellington Zoo.
It was unclear whether penguins had already taken to the four nexting boxes nestled in the front middle of the development.
Kara Puketapu-Dentice said there were regular checks on the area.
"These checks are both regular and ongoing reflecting our kaitiaki obligations as mana whenua, who alongside our development partner The Wellington Company are committed to the protection of the kororā".
Puketapu-Dentice said sniffer dogs were on site this weekend.
"After a suspected sighting of kororā in the weekend, one of our on the ground mana whenua kaitiaki contacted experts to conduct a penguin survey with trained detection dogs."
Developer Ian Cassels or Places for Penguins had not responded to RNZ's requests for comment at the time of publication.