In 2000 Prime Minister Helen Clark was reported as saying that 'It is my strong belief that the days and events around Waitangi Day should contribute to the building of a sense of New Zealand identity and purpose.' In the 21st century the day has been linked more closely with New Zealand identity, and events have expanded beyond Waitangi itself. Protests have continued, and representatives of the Crown have not always been present at Waitangi.
In 2000 the official ceremonies remained at Waitangi. Labour Prime Minister Helen Clark decided to attend a Waitangi Day function at Ōnuku marae, Akaroa, but Governor-General Sir Michael Hardie Boys, some MPs and Jenny Shipley, the leader of the Opposition, were at Waitangi. The programme of events on the Treaty House grounds aimed to make the day one of spiritual observance, ceremony, family fun and entertainment. It was generally successful. An official welcome and forum at Te Tii marae did not run smoothly, and there was an assault on the Waitangi flagpole in the early hours of 6 February. Most media reports focused on these aspects and gave brief coverage to the rest.
The difficulties associated with events at Waitangi and Te Tii marae raised questions about whether official commemorations should continue to be held there. Cabinet decided that in 2001 there would be no official representation at Waitangi, but, in the end, two cabinet ministers were present. The Waitangi National Trust Board organised events to mark the day, including a church service. Although this was disrupted by 300 young people, the rest of the day passed peacefully with games and waka events.
The Crown returned to Waitangi in 2002, with the governor-general, attorney general and prime minister all in attendance. Protestors disturbed the welcome at Te Tii marae and an early church service in the Whare Rūnanga on the Treaty House grounds, but other events were held in a celebratory atmosphere.
Protests have continued at Waitangi, and the prime minister has not always attended events there on Waitangi Day. In 2004 some Māori used Waitangi Day to protest about the government's legislation regarding the seabed and foreshore. In the days leading up to Waitangi Day, National Party politicians were pelted with mud, and members of the government were jostled as they entered Te Tii marae.
Prime Minister Helen Clark did not return to Te Tii marae following the jostling incident in 2004 but did continue to visit Waitangi. Over the next few years her annual Waitangi Day programme generally involved hosting a breakfast at a hotel near the Treaty Grounds and a walk around with dignitaries, before heading to Auckland to attend events there. When criticised for not visiting the lower marae in 2007 Clark responded that ‘the atmosphere is such that if I don't go, there probably won't be incidents and if I did, there would be’.
Māori Labour MPs continued to visit Te Tii marae in the years that followed, as did Opposition leader Don Brash and his successor John Key. Though protest groups continued to gather at the marae the atmosphere was not as heated as it had been in 2004. Many put this down to the growth of the Māori Party, established in July 2004 in protest against the foreshore and seabed legislation. In 2006, by which time the Māori party had won four out of seven Māori seats, Te Tii kaumatua and spokesman Kīngi Taurua commented:
Many of those who used to protest at Waitangi have joined the Māori Party. They now believe they have a voice in Parliament for their concerns rather than having to confront politicians when they come here.
Following the 2008 general election the Māori Party joined a National-led minority government with ACT and United Future. Since forming the government National and Māori Party MPs have continued to attend Te Ti marae, as have Opposition leaders.
In 2009 two men breached the Prime Minister's security cordon outside Te Tii marae and grabbed hold of his jacket yelling that they would not let him on to the marae. The incident was unexpected because of National's new relationship with the Māori Party and Key's recent announcement that he would allow a Māori flag to fly on future Waitangi Days. It was quickly condemned by Māori Party MPs and kaumātua at the marae. Veteran activist Titewhai Harawira was reported as saying ‘that after 30 years of real hard struggle there was no need for physical protest at this time’.
Moves to commemorate Waitangi Day across New Zealand have expanded in the early 21st century. Functions and events are now held throughout the country. The government has made available funding to assist events and activities that acknowledge the signing of the Treaty. The Commemorating Waitangi Day Fund has supported dozens of events, ranging from a commemoration of Lieutenant-Governor William Hobson's journey from the Bay of Islands to Mangungu, where the Hokianga signing of the Treaty was held, to community tree planting, hāngi and kapa haka performances on the West Coast. Events supported by the fund celebrate the positive aspects of Waitangi Day – the coming together of the peoples of New Zealand in a Treaty partnership.
Māori communities have used the day as an opportunity to discuss the Treaty. Some marae hold open days or run talks on the place of the Treaty in New Zealand. New Zealanders elsewhere also now mark the day. There have been concerts in London, as well as less formal activities.