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As he was walking on to the marae guided by Maori Party MP Hone Harawira's mother, Titewhai Harawira, Mr Key was heckled by Mr Harawira's nephew, Wi Popata.
He described Mr Key as "the enemy" and blamed him for numerous ills in society, among them the Foreshore and Seabed legislation which was passed by the previous Labour government.
"Aotearoa is Maori land. It belongs to Maori, John Key," he said, before being ushered away by marae officials.
Mr Popata and his brother, John Junior Popata, were convicted of assaulting Mr Key at Waitangi in 2009 and each sentenced to 100 hours' community work.
Mr Key said he wasn't offended by the protest, saying he had learned from his 2009 experience.
"When I came in 2009, to be perfectly honest it took me a bit by surprise," he said.
"I was coming to the lower marae -- and we hadn't seen that from (former Labour prime minister) Helen Clark for a long period of time -- we'd just signed up with the Maori Party, so it was my expectations for a fairly warm reception, so I've come to learn that there will always be a range of views.
"This time I think there was a bit more tension, I think that reflects that there's tension between Hone Harawira and the Maori Party, but what I do hope is that New Zealand people understand that that is one or two people expressing their views.
"Actually, I got a very respectful hearing (in the meeting house on the marae). I'm not sure that they agree with me, but I certainly got a respectful hearing in the whare and I'm very hopeful the next day and a-half will be a great day and a-half of celebrations of our national day."
Mr Harawira, who is at odds with the rest of the Maori Party over its partnership with National, told reporters he was proud of the protest, though he didn't hear everything that was said.
Maori Party co-leader Pita Sharples was also criticised as the government group was being welcomed on to the marae, with one person calling him "kupapa", or traitor.
Kupapa was a term used to describe Maori warriors fighting on the side of the British during the New Zealand Wars of the 1860s.
Dr Sharples said he was not hurt by the term.
Protest was relatively limited otherwise on the marae, though one banner reading "The Treaty of Waitangi Extinguished 2011, Customary Law Prevails" was unfurled as both Mr Key and Labour leader Phil Goff came on to the marae.
Mr Goff was also questioned inside the marae about the Foreshore and Seabed legislation, which he said in hindsight "was done too hastily".
Labour would look at rectifying anything that has been done unfairly or wrong, he said.
Meanwhile, plans to ask media to pay $1000 to come onto Te Tii Marae eventually did not come to fruition.
Some members of the media were told before proceedings started that they would not be allowed on to the marae. One photographer told NZPA he was not allowed on the marae, and efforts would be made to stop him taking photographs from the road outside the marae.
A few others were allowed on after handing over a koha significantly less than the $1000 which had been demanded.
However, most members of the media found their way on to Te Tii Marae after the Government party had begun its move on to the marae and few had problems from there.