Cr Neil Gillespie, Cr Nigel McKinlay, and Cr Shirley Calvert voted against the move.
''My position to the motion that's being put forward, is not that we shouldn't be helping these communities ... it's just we haven't found the right way to do it,'' Cr McKinlay said.
Cr Gillespie agreed and said the status quo was a ''viable decision'' and until the council had a better understanding of the issue, it should ''park it''.
The Cromwell community had given a ''clear steer'' it did not support it, Cr Calvert said.
Councillors spent more than eight hours in the long-term plan submission meeting yesterday.
Subject to a revenue and finance policy in 2015-16, the council agreed in principle to the subsidisation of the three waters, to be implemented on July 1, 2016.
The proposed uniform charges for water in 2016-17 would be $428, and $460 for wastewater, a combined total of $897.
In 2024-25, proposed charges would cost $1534 combined.
Volumetric and water metering charges would remain additional to the annual charges.
Cr Barrie Wills said they had ''procrastinated long enough'' and were being told by the community to ''get on with the job''.
Cr Malcolm Topliss said there were always going to be ''losers and winners'' and they would never find a time to the implement a policy when everyone was happy.
Central Otago Mayor Tony Lepper said the cost was ''extremely small in the scale of things to come''. About 200 submissions were considered during the meeting, with more than 150 submissions on water charges, including nine oral submissions.
More than half the submissions favoured the a fully subsidised water options, where urban water, wastewater and stormwater charges across the region would be standardised.
Those favouring the fully subsidised option felt it was important to protect smaller communities by spreading the cost of major upgrades to existing water and wastewater systems.
About 23% of the submissions supported a partially funded model, with water schemes paid for by the ratepayers using them, except there would be a cap on how much they paid.
Once the cap was reached, it would be subsidised by the district.
About 10% favoured the status quo, and others suggested alternatives.
Nine supporting oral submissions were also heard at the meeting.
Cromwell resident Charlie Huges told the council people had decided to live in areas where water schemes were not upgraded.
''Why should everyone in the district have to subsidise those who chose not to upgrade?'' he said.
Alexandra resident John Cooney said the status quo was the better option because both water models were not ''well thought out''.
He asked the council to wait until it had a ''better understanding'' of the water funding models.
Cr Clair Higginson said the board was trying to be fair.
Cr Barrie Wills said there were a lot of people in Central Otago, so it made sense that the costs were spread across the region.
The council will meet on June 30 to adopt the long-term plan.
