Police have made three arrests at a Waiheke Island protest where protesters are trying to stop a marina being built.

A group, Protect Pūtiki, has posted images of police at the usually quiet Kennedy Point area.

Inspector Dave Hines said police have arrested three people in relation to trespass.

Hines said there had been ongoing issues for an extended period of time between the demonstrators and developers at the marina site.

"Police have been monitoring the ongoing situation to ensure the safety of everyone involved and our duty is to prevent any breach of the peace," he said.

"Police recognise the lawful right to protest, however we also recognise the right of people to go about their lawful business."

Hines said police were slowly removing a number of staff present, and there has been no disruption to ferry services.

Ngāti Paoa Uri is occupying Pūtiki Bay, saying it is "standing up for the mauri of our ancestral moana that we whakapapa to, ko Tikapa te Moana. Enacting our rights and responsibilities to protect our taonga from the proposed marina, alongside the Waiheke community".

The protesters say a digger has come on to the site to remove 25 rocks while kororā (little penguin) are present.

"Police and diggers have arrived at Pūtiki Bay Kennedy Point on Waiheke Island following an occupation of mana whenua iwi Ngāti Pāoa who are fighting to protect the natural habitat of the endangered kororā/little blue penguin species," protesters said.

Diggers have begun removing rocks while the kororā are present.

"It comes after a long fight against marine developers who were given consent to build Tony Mair's 186-berth marina, but mana whenua said they weren't consulted or part of the planning process," they said.

Green MPs Elizabeth Kerekere and Chloe Swarbrick are calling for work to stop immediately, and for Auckland Council to step in.

Kerekere said developers are breaching their resource consent and are damaging the habitat and threatening the lives of the endangered blue penguins.

"The works must stop. Our people are putting their bodies on the line to protect our taonga and whenua," Kerekere said.

Auckland Central MP Chloe Swarbrick also echoed the calls to stop development and joined the protesters.

Some locals oppose the project, including Mainfreight founder Bruce Plested who called the marine proposal a "disgrace".

"Ngāti Pāoa expects that protectors and protesters will be arrested today," the iwi said.

But Mair says he has a valid consent and is able to carry out the work.

Scott Fickling, Kennedy Point Marina project manager, said a few weeks ago that four trespass notices were issued.

"It is also understood that one person is being sought for arrest and that the police are also looking to speak to two other individuals. These people chose to enter the clearly marked construction zone putting themselves and others in danger. We continue to respect the right of people to protest but our priority remains the safety of our crew, members of the public as well as the protesters."

About five protesters were permanently camped out illegally on the beach, blocking public access complete with cars, caravans and dogs which are being allowed to run off leash. Dogs are known to be a big threat to kororā, he said.

"Visitor numbers to the camp vary from day to day but at the peak there appear to be up to 20 people depending upon the weather."