"We had not previously looked at these North Island bones because the majority are fragmentary or burnt," he said.
"Scouring museum and archaeological records, we found that these waitaha penguin bones were either pre-human, or from the early prehistoric or moa hunter period of Māori culture, between 1280AD and 1450AD."
The team could also show that the proportion of waitaha compared with other birds was high enough to indicate the penguin was probably breeding in the North Island, and weren't just vagrants from the south.
In fact, Rawlence said, the waitaha was likely a "key member" of the lower North Island's coastal biodiversity.
"Elimination of waitaha penguin from the North Island adds to the already significant biodiversity losses from New Zealand, of which the North Island suffered the greatest biodiversity loss after the arrival of Polynesians."
Rawlence said there was still much to learn – and both the waitaha and the hoiho, which remains one of the world's rarest penguins, with a population between 6000 and 7000 – were proving "sentinels of change" for assessing how human impact and climate change have affected New Zealand.
The "cold adapted" yellow-eyed penguin had recently colonised the southern South Island during the so-called Little Ice Age of the last millennium, but was now struggling to thrive, due to unfavourable climatic conditions with increasing sea surface temperature, as well as attacks by predators and fisheries by-catch.
Its inability to adjust to warm conditions likely reflected a combination of factors including rising human pressure and vulnerability to warm temperatures, Rawlence said.
"It raises serious questions about whether yellow-eyed penguins, so called 'native invaders', will be able to adapt to projected climate change in time to avert their extinction on mainland New Zealand, or whether they are a 'mal-adapted' colonisers," he said.
"If they cannot adapt, we may only be able to see yellow-eyed penguins on the Auckland and Campbell Islands."
Rawlence added the study, a collaboration between Landcare Research, Te Papa, Canterbury Museum and Otago University, highlighted the importance of museum collections in helping to answer some of the big questions affecting Kiwis today.
"In this uncertain world, we need to value museum collections," he said.
"None of this research would have been possible without them and the collections teams that manage and curate those collections.
"You never know what you are going to find in museum collections and in the field until you start looking - until a few years ago we didn't think kea were found in the North Island.
"There was one fossil from the height of the last Ice Age from Waitomo but there are now numerous fossils, only a few thousand years old, of kea from the North Island."
