The other mauri stones were buried by Defence Minister Ron Mark.
More than 100 people attended the ceremony, including Prime Minister Jacinda Ardern and students of Whangārei kura Te Kāpehu Whetū, but the exact location of the mauri stones' burial was shrouded behind a screen.
The speakers included Bernard Henare, son of Sir James Henare, the battalion's last commander.
He recalled the formation of a Māori fighting force at the urging of Sir Āpirana Ngata, and how its soldiers had distinguished themselves in North Africa, the Middle East, Greece and Italy.
It suffered the highest casualty rate of any New Zealand battalion in World War II, he said.
For many young Māori joining the battalion was a chance to ''get out of the hills that had hemmed them in all their lives''.
For Sir Āpirana, it was the price Māori had to pay for citizenship of New Zealand — yet when they returned they found little had changed, Henare said.
''They fought and bled in countries with foreign names ... but they kept their mana, they kept their spirit, they acquitted themselves well as men and as warriors.''
Ron Mark said he hoped the new museum would remember not just Māori who had fought in World War II but those who fought in every overseas conflict before and since.
Although based in Northland, the home of A Company, the museum will tell the story of all four companies.
The mauri stones were collected from sacred sites around the Ngāpuhi rohe. Two were taken from a place on Motatau Mountain were warriors used to bathe before battle. The last person to complete that ritual was Sir James Henare.
Only one other veteran of the battalion's original 3600 soldiers is still alive. C Company's Epineha Ratapu, 97, of Masterton, was unable to travel to Waitangi to take part in the ceremony due to ill health.
Watchman Waaka, of D Company, died in Hokianga on December 11 last year. He was 96.
