By the 1840s, Waitaha primarily occupied the land between Tauranga harbour and Te Puke. During the 1840s and 1850s, the Waitaha leader and prophet, Hakaraia, preached peaceful engagement with Pākehā.

When Crown forces invaded the Waikato in July 1863 a number of Waitaha fought for the Kingitanga, while some sided with the Crown. Others remained neutral. These internal divisions created enmity amongst Waitaha and also with neighbouring iwi.

War came to Tauranga in 1864. Hakaraia was a spiritual leader for the Māori force which defeated Crown troops at Gate Pā in April. When Crown troops defeated Kingitanga Māori at Te Ranga in June, Waitaha men were among the casualties.

The Crown regarded those Māori who fought at Gate Pā and Te Ranga as rebels. In May 1865, the Crown confiscated 214,000 acres of land around Tauranga including land in which Waitaha had customary interests. The Crown announced that it would retain only a quarter of the confiscated land and that the remainder would be returned to Māori.

Hakaraia rose to prominence as a leader of the resistance to the survey of confiscation. In January 1867, government forces assaulted Waitaha settlements near Te Puke, destroying houses, crops and livestock as ‘a special punishment’ for Hakaraia. Using scorched earth tactics the Crown pursued Hakaraia to his death in 1870.

In 1868 the Crown extended the boundary of the confiscation district by 75,000 acres to include much land claimed by Waitaha and also Otawa, a maunga sacred to Waitaha. The Crown accepted the ancestral claims of Waitaha to approximately 25,000 acres in the confiscation district but withheld much of this ‘in payment for the sin’ of Hakaraia.

The Crown opened negotiations with Waitaha for Te Puke in 1873 before the Native Land Court had determined the block’s ownership. The Court, which was created under the native land laws introduced by the Crown in the 1860s, was established to convert customary title, which was communal and fluid, into individualised and permanent titles derived from the Crown.

Waitaha did not initially wish to sell or lease Te Puke. However, in September 1873, rival claims over the land motivated Waitaha to sell part of the block. The Crown pressured Waitaha into selling more land and told Waitaha the block would be mortgaged to the government if they did not sell, on account of a survey debt owed by another claimant to Te Puke.

Waitaha were by this time suffering great economic hardship and wanted the Crown to pay the balance of the purchase money without waiting for the Court to determine title. When the Crown refused, Waitaha tried to withdraw from the sale in order to sell to a private party. The Crown would not relinquish its purchase and barred private parties from attempting to acquire the land. The Native Land Court eventually awarded title to Te Puke to Waitaha in October 1878. The Crown completed its purchase over the next eight years.

Waitaha took part in many Native Land Court hearings in the 1880s and early 1890s. Most of the land Waitaha were awarded was sold in the 1880s and 1890s, largely to the Crown.

By the end of the nineteenth century Waitaha had insufficient land and resources to sustain the tribe. According to Waitaha, this forced some members of the iwi to follow other tribal affiliations. Waitaha express this impact in the whakatauki “Ko Waitaha te iwi, he tangata ngakaurua”: Waitaha was once a powerful tribe, but because of the loss of land they became fragmented and have never been able to unite again.