The councils' and DoC's costs escalated when landowners opposed the change in governance, which they felt gave unfair preference to iwi, and eventually blocked access to the fence from their properties.
Equal representation was reinstated last year to resolve the issue but four landowners are still refusing access to the fence.
Greg Martin, Waikato conservator and one of the trust's founding trustees, said DoC's extensive investment had contributed to an "internationally significant conservation project".
But former trustee Fiona Judd, removed from the trust in 2010 when she opposed the governance change, feared ratepayers and taxpayers would continue to have to cover the shortfall.
The trust had shut itself off from $600,000 a year in operational funding and $4 million in capital funding from corporates because of the governance issues.
"Their [the trust's] vision for the project encompasses only the idea of a community-funded project. They have lost the faith of numerous corporate sponsors ... Therefore they have missed out on big money, but they are happy for the shortfall to fall back on ratepayers and taxpayers."
Trust co-chair Tony Wilding said it was aware the councils couldn't go on funding it forever and a new visitor centre due to open at Christmas was part of a plan to bring in revenue and boost tourism.
Adding up
* $26m - total spent on the island to date.
* $4.3m - from Waikato Regional Council.
* $1.7m - from Waipa District Council.
* $900,000 - from DoC.
* $1.5m - annual operational cost.
* $14-16m - to build fence.
* $1m - on new visitor centre.
* $50,000 - annual cost of staff to monitor fence where surveillance wire has been cut.