That was a reference to the bitter standoff between the Tuhoronuku and Kotahitanga groups over the mandate. Several hapu, led by Ngati Hine, have objected to the negotiations and the mandate given and are waiting on an urgent inquiry by the Waitangi Tribunal.
Sir Jerry said other settlements showed the progress that could be made. "These are all examples of the hope that we can share."
Ngapuhi elder Kingi Taurua said he was surprised by Sir Jerry's comments.
"I'm very surprised he spoke about it. He shouldn't be talking about that. This is between us and the Government. It's wrong for him to make that statement. The Governor General doesn't have any right to talk about it."
Earlier on the marae, Mr Taurua also raised the Government's response to a Waitangi Tribunal finding that Maori chiefs had not ceded sovereignty when singing the Treaty.
He also objected to Sir Jerry's plans to attend a ceremony at Mangungu Mission in the Hokianga to mark the 175th signing of the Treaty. Mangungu Mission was the site of the largest signing of the Treaty on February 12 1840. Sir Jerry is the first Queen's representative to visit since that signing.
Mr Taurua said Waitangi was where the Treaty was negotiated and first signed and where it should be commemorated.
Sir Jerry responded by saying he would also visit Waitangi first but intended to visit the sites of many signings this year.
Sir Jerry ended his speech with a rather risque joke - saying he recalled Winston Churchill's advice that "a speech should be like a woman's skirt - long enough to cover the subject but short enough to keep interest."
When asked about it this afternoon, Prime Minister John Key said Sir Jerry's comments were "totally appropriate".
Mr Key said he didn't read them as political comments, but more as personal comments to give "hope and aspiration for the people of the Far North".
"I don't think he was making political comments, my read of his comments is he was simply putting his own emphasis, that settlement would be an important step for economic growth and development, and for opportunities, in the Far North."
He is probably reflecting on the fact that large iwi like Tainui and Ngai Tahu have settled, and have gone on to have significant financial resources which they have been able to deploy for their people."
He said although it was unusual for Sir Jerry to comment on matters such as these, in his role as Governor General he was "quite entitled" to share his hope and vision for the country.
- additional reporting Audrey Young