In the two decades after the signing of the Treaty of Waitangi in 1840, Ngati Whare were mainly left alone from colonial interference, secure in their inland, mountainous, and frequently bush-covered territory. Ngati Whare, though, welcomed Christian teachings and the peace that they helped establish, having the missionary James Preece reside with them from 1847 to 1853. One Ngati Whare leader of the time, Matiu, became a Christian teacher, later adopting Pai Marire beliefs. Matiu was shot by colonial forces in 1869.
Being wary of colonial encroachment, Ngati Whare supported the establishment of the Kingitanga in the late 1850s. After the Crown's invasion of the Waikato in 1863, Ngati Whare fought against the Crown in various ways, supporting Tainui forces at the battle of Orakau in 1864, fighting against Ngati Manawa and Te Arawa forces at Te Tapiri in 1865, and offering succour to the prophet Te Kooti during the Crown's relentless pursuit of him through the Urewera and central North Island regions between 1869 and 1871. Ngati Whare fighting chiefs of this period included Hapurona Kohi, Hamiora Potakurua and Mauparaoa.
In May 1869 colonial troops led by the butcher of Nga Tapa, Colonel Whitmore, launched a surprise attack against a Ngati Whare pa at Te Whaiti, named Te Harema (or Salem). During the attack the half dozen or so mainly older Ngati Whare men in the pa were shot down as they tried to escape. The women and children of the pa were taken hostage. Whitmore passed the hostages into the keeping of his Te Arawa auxiliaries so, in his mind at least, Ngati Whare might be destroyed as a tribe. The women and children were later allowed to return from captivity, but only after the remaining men of Ngati Whare had themselves "come in" and surrendered to the colonial forces in a one-sided peace.
Through the latter 1870s and 1880s Ngati Whare and other Urewera communities were left mainly alone by the Crown, out of sight and to a certain extent out of mind. From the late 1870s through to the early 1890s, the Native Land Court began its work around the Kaingaroa and upper-Rangitaiki region. Various blocks passed through the Court, including Kaingaroa No.1, Kuhawaea, Heruiwi, Pohokura, Whirinaki, Heruiwi 4, Runanga, and Pukahunui. This was mainly done at the behest of Ngati Manawa leaders, who had had resolved to engage directly with the new colonial institutions as a way to secure their future. Many Ngati Whare affiliated persons were put on the title to these lands side by side with Ngati Manawa. Unfortunately, though, the Court was a Trojan Horse, ultimately facilitating a wave of Crown purchasing and land alienation.
In 1894 Premier Richard Seddon visited the Urewera in a diplomatic push to invite the iwi of the region to cease their isolation and come "under the law". Up to then it could not be said that the "Queen's writ" ran in the Urewera. At Seddon's invitation, and after a number of meetings up to 1896, both Tuhoe and Ngati Whare endorsed the creation of the Urewera District Native Reserve as a means to protect the remaining lands of the Urewera from alienation. This Reserve was unique in the history of New Zealand, being the only moment when a substantial level of autonomy and self-government was delivered, through Parliament, to the Maori people.
A few years later, however, the Crown went back on its promise of protection, commencing a series of illegal and aggressive individual purchases in the Reserve, while at the same time preventing the lease of lands or other means of revenue generation such as forestry. Retrospective legislation was passed in 1916 to make the Crown's actions "legal". Under a continually enforced monopoly, the Crown's now "legal" purchases continued up until 1921, when it "consolidated out" its interest in the land from the remaining non- or part-sellers.
The Crown's purchase and consolidation process saw most of the Urewera Native Reserve cut up and sold to the Crown alone, at prohibitively low prices and with burdensome survey and other costs. Ngati Whare was left with a small area of land, entirely insufficient to sustain them as an iwi.
Ngati Whare leaders later protested about these purchases, describing them quite simply as "theft". No compensation was ever paid, though, even for the Crown's acquisition of the enormously valuable podocarp forests of Te Whaiti at a price that was well below market value. Expert valuation research conducted in the early 1990s concluded that Ngati Whare was ripped off to the tune of around £234,000, as at 1918 prices.