But in a further series of blows to the council, Justice Young said even if he was wrong on those points the case would have failed because when making each of those decisions the Government would not have been acting inconsistently with the Treaty of Waitangi. He also found against the council's other arguments.
However, the council and its allies vowed to fight on.
Council deputy chair Rahui Katene said Justice Young had relied on "statutory technicalities".
"We think that the view taken about the statutory framework does not fit with previous court decisions and we are now working on an appeal."
Council lawyer Felix Geiringer said he had already begun that work. But while he last month raised the possibility the council would bypass the Court of Appeal and take its case directly to the Supreme Court, that decision had yet been made he said.
The council would have to apply for to go directly to the Supreme Court which was "not something you take for granted".
"Whilst it's still being considered just because of the time issues involved, it's still quite likely that this case will instead go to the Court of Appeal."
The council would reveal its decision within a few days.
Tamati Cairns, chairman of the Waikato River and Dams Claims Trust and Pouakani Claims Trust which pursued the court action alongside the council, said he would support an appeal to the Supreme Court.
He said Justice Young's decision held no surprises.
"the Judge forecast his views during the hearing which I attended throughout".
However he noted comments by Justice Young in his judgement that it was a "great sadness" that many Maori water claims "have not been heard or resolved."
Justice Young went on to "urge those who have the authority to urgently address these claims."
Finance Minister Bill English and State Owned Enterprises Minister Tony Ryall said the decision vindicated their view that the asset sales programme would not affect the Crown's ability to recognise rights and interests in water, or to provide redress for them.
Mr Ryall said the Government's share offer programme remained on track with Mighty River shares expected to go on sale between March and June next year.
"If the High Court decision is appealed, we hope this can be heard as soon as possible."
Labour's SOE spokesman Clayton Cosgrove said the High Court's decision was "just the first in a number of steps for this appeal to go through".
"It is likely there will be an appeal and New Zealanders will again have to fork up the costs of court hearings."