"This confusion resulted in too little provision for growth and the current housing challenges.
"The strength of a single Auckland Council is that this issue will be resolved."
The minister said the Government would be giving the council distance to make a considered decision on the plan.
The panel today recommended more urban sprawl, greater densification, and the provision of 420,000 new dwellings in Auckland over the next 24 years.
Labour leader Andrew Little welcomed recommendations to scrap restrictive controls which stopped Auckland growing up and out.
"The pressure is now on Auckland Council to do the right thing and back the recommendations," he said.
However, Little opposed the panel's recommendation to remove affordability requirements for large-scale developments - a change which was requested by Government agencies.
At present, at least 10 per cent of properties in new housing developments must be in the affordable range, which is less than $600,000.
The Ministry of Business, Innovation and Employment and Housing New Zealand asked for this rule to be scrapped, and the panel agreed.
"It beggars belief the Government asked the panel to scrap affordability requirements when Auckland is desperately short of affordable housing," Little said.
Labour also wanted the panel to go further by getting rid of the city's urban growth boundary.
Green Party co-leader Metiria Turei said her party was pleased about proposals to build more homes in existing suburbs and close to workplaces, but it had concerns about other provisions including protection for significant Maori sites.
Recommended zoning plan for central Auckland (Waitamata region)
Recommended zoning plan for Auckland