An investigation into claims 49 cows were buried in a hole dug at Motutapu Island without consulting iwi or Heritage New Zealand - potentially damaging an archaeological site - could result in criminal prosecution.

Ngāi Tai ki Tāmaki Tribal Trust alleges the cows died on Boxing Day last year after battling 26C heat and a large hole was dug for them to be buried at an archaeological site.

But the Department of Conversation has rejected the claims, saying the cows died from eating fruit from sycamore trees and were accidentally buried on a corner of an archaeological site, which was only identified during the Heritage New Zealand investigation.

Heritage New Zealand (HNZ), on the request of Ngai Tai, launched an investigation into the deaths and, according to the trust, confirmed to both the trust and DOC in May that the allegations were correct.

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"HNZ confirmed that a hole had been dug to accommodate the burial of 49 dead cows and that there seemed to be some damage to a midden site within the burial. There was no legal or formal application to HNZ," Ngāi Tai ki Tāmaki Tribal Trust chairman James Brown said.

"Ngāi Tai have now waited six weeks since meeting HNZ and the Department, without being any closer to understanding what happened, where, by whom and at what cost. We have no answers."

Brown said Heritage New Zealand told the trust at the end of June it was still waiting on information from both Motutapu Farms which manages the farm and the Department of Conservation, which owns and manages the island.

"Unfortunately HNZ has not set clear timeframes or conditions around the information requested, as Ngāi Tai became aware of on 22 June 2018."

Heritage New Zealand acting mid-Northern area manager Ben Pick confirmed it was investigating allegations there had been damage to an archaeological site on Motutapu Island due to the burial of animals. The investigation included site visits and information gathering and was still on-going.

Pick said Heritage New Zealand took allegations into site damage very seriously and any damage to an archaeological site by any person who knows or suspected the site was an archaeological site was an offence under the Heritage New Zealand Pouhere Taonga Act 2014.

He could not confirm when the report would be completed because it needed to ensure it was a detailed and comprehensive investigation given that unauthorised damage was a criminal matter.

But DOC Auckland Inner Islands operations manager Keith Gell said a vet had established the cows died from eating fruit from sycamore trees growing on Motutapu island, not from heat as Ngai Tai alleged.

Gell said the farmer followed the correct procedure and consulted a map showing known archaeological sites on Motutapu before burying the cows. However, had been unaware the spot he had chosen had a midden hidden underground as it was not identified on the map. Middens contains shells and other food refuse left by early Maori.

"This slight accidental disturbance of the corner of the midden was discovered by Heritage New Zealand," Gell said.

But Brown said they had struggled to get any answers from DOC for almost seven months. He said the public had the right to know what was happening especially given DOC's ongoing reminders to Ngāi Tai that there was a wider public interest in its ancestral landscapes.

Ngāi Tai has also asked Heritage New Zealand to investigate whether large plantings of native forestation carried out on the island had the appropriate approvals. However, Heritage New Zealand said other activities on the island were not part of this investigation.

A Ministry for Primary Industries spokesperson said MPI had only been made aware of the deaths today, and as a result had begun making inquiries into the deaths of the cattle.