Last week at Waitangi, Prime Minister John Key offered and advance payment on the eventual settlement as an incentive for the iwi to put aside its differences and move forward with its claim.
Yesterday Mr Finlayson and Dr Sharples said that the process by which Tuhoronuku was selected was "fair and in good faith".
However as a result of feedback during that process, "Tuhoronuku has modified its proposed structure to increase hapu representation, and how the mandated group will make decisions".
"It will also be separated from the Runanga and be governed independently by a new board which will be freshly elected."
"For these reasons and complying with the requirement for the Crown to also act in good faith, the Crown has recognised the mandate of Tuhoronuku to negotiate a settlement of the historical Treaty grievances of Ngapuhi."
The Government hopes to conclude a settlement with Ngapuhi this year.
Ngapuhi runanga chairman Sonny Tau last week said the iwi was seeking a settlement worth about $500m which would dwarf previous deals. Mr Finlayson, however, has indicated that is highly unlikely.
A Ngapuhi settlement and the resources it would bring are widely seen as a key step in developing Northland's sluggish economy and tackling the region's high Maori unemployment rate.
Tuhoronuku last night said recognition of its mandate signalled "a new era of economic prosperity and social and cultural advancement" for Ngapuhi.
Mr Tau said: "We encourage all Ngapuhi to stand firm behind Tuhoronuku as it fights the Crown for the best possible settlement".
Pita Tiipene, spokesman for Kotahitanga, the hapu-based collective which opposes the runanga's dominance of talks with the Government, said a legal challenge to the Government's decisions remained a possibility.
He was glad to see a provision for hapu to withdraw from the mandate given "the comprehensive opposition to Tuhoronuku by the confederation of Ngapuhi hapu".
"Until our people have had a chance to digest the conditions, we can't provide a clear response but legal action remains a distinct possibility given that the Crown continues to ignore the will of the people and instead remains steadfast in their desire to push things though for political reasons in an election year."