The GWRC applied for a super-city council that merges all councils and creates nine local boards.
Carterton Mayor Ron Mark said it was highly likely the commission would stick with the status quo.
"I think the sad reality is that anything that is demanded to be an option, and not supported by the majority of Wellington metropolitan people, is likely to be rejected," Mr Mark said.
That would leave the status quo even if Wellington supported Wairarapa's application, he said.
Many of the applications supported Wairarapa's wish to go it alone. "The ironic thing about that is the vast majority of those people do not object to our application, but that won't matter," said Mr Mark.
"My fear is that after all this time, of three years of hard work and, most importantly, finally getting the vast majority of councillors to a point where they agreed there could be unification, we may have a proposal that is not possible for them."
He said Parliament had passed "fundamentally flawed" legislation - the Local Government Act was adapted catalysing the reorganisation process. There could only be one option, he said.
"If it's in any way or shape a super-city, my belief is it will fail."
Mr Mark said all the evidence from polling had shown the majority of the Wellington region did not want a big super-city and the vast majority of Upper Hutt did not want any change.
He said the councillors against a unitary authority did not understand the legislation and were using it as a political point.
Wairarapa people need to govern Wairarapa and under a super-city having one or two local boards would be inadequate, he said.
"That message came through quite clear."
South Wairarapa Mayor Adrienne Staples said central government wanted to see streamlining of local government and the status quo was unlikely.
"At the very least they would call for a reorganisation of the three Wairarapa councils."
Mrs Staples said she was certain that any proposal from the LGC would go to a poll and she did have some concerns about it.
"That poll is held for a LGC proposal against the status quo.
"My biggest concern is that if they put forward a proposal that does not have support of the people it will fail at the poll and we will be back to square one, having achieved nothing after three years of work."
Masterton Mayor Garry Daniell said the process was entirely in the hands of the LGC.
"Some concerns have been raised about pre-determination, but we have been assured in all our dealings with the LGC that they have a very open mind with regards to the best option for the Wairarapa community."
He said the council was confident its joint application was robust.
In Wairarapa, almost $780,000 has been spent on public consultation, compiling reports about the viability of a unitary authority and lodging a proposal with the LGC.
Wairarapa Governance Review Working Party chair Jane Terpstra said it had dedicated thousands of hours to the project outside of normal council business. The costs had been met from existing budgets.
