The measure will be introduced for council elections in 2007
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Ministers have been warned against introducing proportional representation for local government.
The Scottish Convention of Local Authorities (Cosla) said the move had little support among voters.
Speaking at the Scottish Labour Party conference in Inverness, Cosla president Pat Watters urged the Scottish Executive to reconsider.
The measure forms part of Labour's agreement with its Liberal Democrat coalition partners.
The single transferable vote system will see the creation of larger wards represented by three or four councillors in 2007.
Labour was not in favour of the move but made a concession to the Lib Dems in order to form their coalition.
But Mr Watters said he believed voters wanted more important issues addressed.
"Not one person has come into a surgery to see me about the voting system," he told delegates.
"They come to see me about services like education and roads."
Mr Watters claimed the move would damage local government and change a system which makes councillors accessible and accountable.
"If it's important that we drive forward Labour values within the executive, why is it any less important that we drive forward those same Labour values
within local government?" he asked.
"We are not a creature of the executive, we are a creature of the electorate and it's important we remember that.
"PR will not take forward democracy in local government."
On Friday, Finance Minister Andy Kerr told the conference that PR for local government was the price of coalition government.
Few Labour activists support the measure, but those who want the status quo did not call for a vote.