Archaeologist Michael Taylor has been to have a look, and written a report.
He said the company harvesting forest there during his visit, Erni Logging, was helpful.
HNZ will not release the report or name the landowner while the matter is being investigated, Central Region manager Karen Astwood said.
Under the Heritage New Zealand Pouhere Taonga Act 2014 it is unlawful for any person to modify or destroy, or cause to be modified or destroyed, the whole or any part of an archaeological site without the prior authority of HNZ.
An archaeological site is a place associated with pre-1900 human activity, where there may be evidence relating to the history of New Zealand.
Neilson discovered logging happening across the former pā site when he went to meet Ngā Rauru people on their annual Waitōtara Awa Hikoi about three weeks ago. He said it is one of many examples of damage to places important in his tribe's history.
"Just up the road from our Waipapa Marae is Tieke, one of the most sacred sites in Rauru. It's been cut in half. They had to widen the road and there was only one place to go and that was Tieke. No notice was given, there was no consultation," he said.
There are a lot of archaeological sites in the Nukumaru/Waitōtara area. When Colin Smart surveyed 72 square miles in the early 1960s he found an average of 3.5 sites per square mile, and a total of 48 pā.
Tarata Pa stretched a along a ridge and down to the Waitōtara River, about 15km from Waitōtara Village. It was the home of Ngāti Ruaiti, Neilson said, in a larger Ngāti Pourua area. There was a papakainga (village) at its base, and a wetland extending up the valley.
"There would have been plenty of kai."
Ruka Broughton tuarua (the second) told Neilson how people defending the pā once threw hāngi stones down on attackers. A karaka tree nearby is the biggest Neilson has ever seen, and he said karaka are found near most pā in the Aotea region.
Tarata Pa looked more prominent before pines were planted across it in the 1990s. In the early 1960s the hills were grazed by sheep and the outlines of former ditches, flat areas, terraces and storage chambers dug into the sandstone hillside were well preserved.
Between 1960 and 1962 archaeologist Colin Smart did some excavations across one area, lasting four months and involving 50 people. The digs were supported by the Dominion Museum and National Historic Places Trust.
He found the remains of buildings, ovens, hearths and 47 pits or chambers for storing water and kumara. There was the remains of an eel weir in the river, and four canoes at the foot of the pā.
There were also artefacts - adzes, chisels, grindstones - and food remains - shells and a few bone fragments, including crushed and burnt human bone.
The Waitōtara Valley Rd has cut through the ridge more than once, damaging the pā. But when the New Zealand Archaeological Association visited in 1987, most of it was still intact.
Then in the 1990s the ridge was planted with pine trees, which are now being harvested. Tracks have been cut across the pā.
One end of the ridge, still in trees, has yet to be harvested, and Neilson fears more damage will be done when that happens next year.