Throughout the morning Mr Tamaki sat at the front of the marae alongside Dame Te Atairangikaahu, a position of symbolic prominence.
The seating arrangement is understood to have confused some invited guests and dignitaries, as well as some Maori close to Dame Te Ata's inner circle.
A spokeswoman for Maori Affairs Minister Parekura Horomia said Mr Tamaki had been invited by the Queen to sit next to her "as a matter of courtesy". That was not unusual.
Foreign Affairs' chief of protocol, Tia Barratt, said Mr Tamaki had been at the pre-breakfast ceremony where he had conducted prayers on behalf of guests.
Afterwards, Dame Te Ata had simply asked Mr Tamaki to take a seat next to her during the Prime Minister's welcome.
The offer came about because he was the head of the Destiny Church, "not for political reasons".
Destiny Church was at the forefront of opposition to the Civil Union Act, and 6000 people marched on Parliament to oppose the bill in 2004.
It has promoted "traditional family values", described the Government as having "gone evil", and has attacked a "radical homosexual agenda".
Its political wing, Destiny NZ, stood candidates in the last general election.
Mr Tamaki's prominence alongside Dame Te Ata was treated with a great deal of sensitivity among members of Tainui last night.
Chief executive Hemi Rau said: "In all honesty it's not my place to make any comment whatsoever regarding the place of Brian Tamaki."
One member of the Government party said some ministers had been annoyed to be told Mr Tamaki had criticised the Government's stance on "moral" issues - such as the civil union law - before they arrived.
However, it was up to the Queen to determine who her guests were and where they were seated. The Government was well aware Destiny played an important role in the lives of a number of tribal members.
Richard Lewis, leader of the Destiny NZ party, said Mr Tamaki had been invited to the event several weeks ago "by the Queen herself".
"How else could he be sitting next to her? He sat with her through the whole thing - from the pre-breakfast this morning at about 7am for the duration of the occasion. He ... spent the day, at her invitation, pretty much at her left-hand side."
Mr Tamaki's Destiny Church has built up a significant following in recent years, especially among Maori.