The Home Owners and Buyers Association says thousands of leaky homeowners may face additional financial hardship if it is found they used private certifiers on their homes.
The warning comes as Tauranga City Council says it has no financial responsibility for those homeowners who used private certifiers rather than council-provided certifiers.
The Government last month announced a package under which it and local authorities each pay 25% of repair costs and homeowners pick up the remaining 50%.
However, only those whose homes were certified by a council building inspector are eligible for the contribution from the local authority.
Tauranga City Council's dispute resolver, Terry Wynyard, told Nine to Noon that 75% of its new homes were signed off by private certifiers in the 1990s.
"The Building Act provided that regime, gave the Government the ability to set up the agency, the Building Industry Authority, who registered, maintained the register and were responsible for any disciplinary processes under that regime," he said.
The president of the homeowners and buyers association, John Gray, says in some cases it's been difficult to establish whether a private certifier was used.
Mr Gray says the Building Industry Authority also failed to ensure private certifiers had insurance.
He says local and central government are out of touch about how some homeowners are supposed to meet 75% of their costs.