The Ka Mate version of the dance was devised by Te Rauparaha, the warrior chief of the Ngati Toa, after he escaped death while being chased by his enemies in the early 19th Century.
It has since been performed by the All Blacks as a pre-match challenge to their opposition.
Versions of the Ka Mate used in recent advertising campaigns by have deeply offended the Ngati Toa tribe who claimed the adverts made light of the haka's cultural significance.
A 2006 advert from Italian car giants Fiat saw a number of women performing the traditional dance, which is only allowed to be performed by men. A year later, a bakery produced an animated commercial with gingerbread men performing the haka - something which was met with outrage by the Ngati Toa.
The Ngati Toa tribe has made several attempts to trademark the Ka Mate over the last decade but they have been unsuccessful on each occasion.
Today's move to give the intellectual property rights of the challenge to the Ngati Toa is part of a larger agreement to settle grievances going back 160 years, which sees the tribe receive land around the bottom of the North and top of the South islands, as well as a payment of $63.72 million USD.
Although the agreement will protect the Ka Mate from "inappropriate use", New Zealand Prime Minister John Key said he did not expect the Ngati Toa to be able to claim royalties nor veto its use by the All Blacks or other parties.
"It would be unacceptable for the Crown if there was a charge on New Zealanders or a restriction on New Zealanders for them to have a rendition of Ka Mate," said Key.
A haka of some description was first used by New Zealand touring teams as far back as 1884, but the use of the Ka Mate version of the dance at the beginning of an international match is thought to have first been employed when the All Blacks faced Scotland on the 1905 overseas tour.
When a New Zealand Army team played Wales in 1916, the words of Ka Mate were included in the printed programme, suggesting that it had by then become an integral part of New Zealand teams playing overseas.