Twenty-one bodies were recovered from the rocky coast at Doctors Point on Saturday, another seven on Sunday and two yesterday.
Department of Conservation partnerships ranger Simon Alefesio-Tuck said rangers were alerted after a member of the public called the Doc hotline on Saturday.
The bodies of the penguins, which had puncture wounds around their necks, had been sent to Massey University for autopsy.
The cause of their deaths could be known today.
Mr Alefesio-Tuck said they were killed by an animal, but he could not confirm what sort until the autopsy results were in.
The dead penguins were spread around the rocky shore towards the Mapoutahi Pa headland, a breeding area for the birds, which were nesting at this time of year.
The area was a popular dog walking spot and he asked owners to watch their pets.
''We are urging people to keep their dogs under control, definitely keep their dogs in sight and ensure they are secured on properties, especially at night, and to report any stray or uncontrolled dogs in the area.''
Marine wildlife was occasionally killed by other animals, but mass deaths were rare, he said.
Dunedin city council animal control team leader Ros MacGill said even though it was not clear the culprit was a dog, animal control had increased its patrols of the semi-rural area as a precaution, to one patrol a day.
• The Doc emergency hotline is 0800 DOCHOT (0800 362-468).
