"MWH and Napier City Council have used different methodologies and asset valuations to derive their figures," commission chairman Basil Morrison said.
"Local government infrastructure renewal and asset valuation is a highly complex area.
"Even if the commission was to use the Napier methodology and resulting figures, the decision to propose ring-fencing of assets and debt would remain valid. It is based on the fact that each council, and their ratepayers, is starting from a different position."
Napier Mayor Bill Dalton said his council would engage independent consultants to review the figures used by MWH and the commission, and to review the process and methodology behind the study and the commission's report.
"It's going to take a few days for us to get that done," he said.
"The LGC seem to have set out to try to undermine our reputation to push their own cause.
"They are determined to try to show our position as being a negative one when, in fact, we are in a very positive position."
Wairoa Mayor Craig Little said he was looking forward to the material being reviewed.
Wairoa District Council chief executive Fergus Power said the council maintained its view that the figures used by the commission were wrong.
"We're quite happy to have our views validated and if the LGC continues to stand behind what was done then that certainly raises issues when it comes to any judicial review that may occur in the future," Mr Power said.
The chairwoman of pro-amalgamation group A Better Hawke's Bay, Rebecca Turner, welcomed the commission's announcement.
"The fact that we've now got clarity on all the councils' financial states is seriously welcomed, as is the Local Government Commission's decision on ring-fencing," she said.
The commission will do a survey of 2000 Hawke's Bay residents to gauge support for its proposal.
"The ring-fencing proposal is just one aspect of that reorganisation. The results of the survey will be weighed up with all other relevant information before the commission makes any decisions on its next steps," Mr Morrison said.