Kūkūtai's father, also named Kūkūtai, was a warrior of very high standing, and a leader of Ngāti Tīpā of Waikato, who were settled along the coast from Kāwhia Harbour to Waikato Heads, and along both banks of the Waikato River to Onewhero, above Te Kōhanga. When his father was killed in 1846, Kūkūtai was elected to his place, over his elder brother, Erueti. Kūkūtai's mother was Oeroa, and he was married twice, to Rangiherarunga and to Rangihaia.
Kūkūtai was converted to Christianity by the CMS missionary Robert Maunsell, who had set up a mission station at Maraetai, at Waikato Heads, in 1839. Kūkūtai took the name Waata (Walter). Later he also used the name Pihikete. When Maunsell's assistants, C. S. Völkner and J. W. Stack, moved upriver from Maraetai to Te Kōhanga in 1853, to prepare the ground for Maunsell to follow in 1854, Kūkūtai moved his whole tribe there. He built a church on his own land at Te Kōhanga.
On 20 April 1853 Kūkūtai gave 750 acres of land at Te Kōhanga to the Crown as a site for a Church of England school for both Māori and Pākehā children. He banned alcohol from his jurisdiction, and built himself a European house. In 1857, when F. D. Fenton arrived in Waikato to advise on and set up judicial institutions, Kūkūtai was appointed an assessor, a position with some of the duties of a magistrate. He was also elected manager of his tribal farm. At the great meeting of Māori leaders at Paetai, near Rangiriri, to discuss proposals for a Māori kingship, in 1857, Kūkūtai led a contingent which paraded under the Union Jack. Although opposed to land-selling, he spoke against the establishment of the kingship, and supported Fenton's appointment as resident magistrate in Waikato.
Partly as a result of the Paetai meeting, a system of tribal councils (rūnanga) was set up. When Governor George Grey visited Waikato in December 1861 to attend a great meeting of Waikato people at Taupari, near Te Kōhanga, and to make known his intentions regarding the Māori kingship, he installed Waata Kūkūtai as head magistrate of the Taupari rūnanga. Kūkūtai drew a salary of £50 per annum.
Kūkūtai gained a reputation as something of a spendthrift. He borrowed his salary in advance from the government, and was considered by the Waikato resident magistrate, John Gorst, to be conceited and self-serving. When British forces invaded Waikato in July 1863 Kūkūtai and Te Wheoro built and occupied a pā at Te Ia (Havelock, near Mercer). They transported supplies for the British from steamers at Waikato Heads upriver to the Camerontown redoubt, until the supply line was severed by a Ngāti Maniapoto attack in September. Kūkūtai received the rank of major in the New Zealand militia. His salary was raised to £150 per annum and he also applied for a salary for his wife, because his public duties prevented him from growing food for her.
In 1865 and 1866 Kūkūtai and the Taupari rūnanga were engaged in building a school and attempting to recruit a teacher. Kūkūtai wrote several times to Bishop G. A. Selwyn requesting his support and assistance. In December 1866 he wrote to Selwyn stating that in depression after the death of his wife he had taken poison and would shortly die. He was removed to Waiuku, where he died on 8 January 1867, at the estimated age of 45. He was succeeded as leader of Ngāti Tīpā by his nephew Hōri Kūkūtai.