The Taxpayers' Alliance said David Crawford topped its Town Hall Rich List, after claiming the retired Glasgow City Council director got £486,303 during 2012-2013, including the terms of his redundancy package.
The right-wing group, which campaigns for small government, also labelled Glasgow the council with the most staff in receipt of remuneration over £100,000, but the figure was denied by the local authority.
The Alliance said there were 52 councils with at least 10 employees getting more than £100,000 and 2000 council workers overall getting more than six figure pay.
It said the highest-paid council employee, excluding larger than usual, one-off payments due to redundancy or retirement, was Ian Craig, managing director of Lothian Buses, which is 91 per cent owned by the City of Edinburgh Council
The group said Mr Craig received £300,081.
A Glasgow City Council spokesman said: "We do not employ 32 people who earn over £100,000 per year; we employ eight people on such a salary.
"The Taxpayers' Alliance has artificially inflated its figures by including the results of the council's early retirement programme, which will actually save taxpayers £55m in wages every year."
The 2012-13 Town Hall Rich List identified 2181 staff who received remuneration six-figure remuneration, down from 2295 the year before.
Jonathan Isaby of the Alliance said it was good news the figure was falling and suggested it was because many authorities had finished paying "eye-watering" redundancy bills.
He added: "Sadly, too many local authorities are still increasing the number of highly paid staff on their payroll. It's particularly galling in places where councils are pleading poverty and demanding more and more in council tax. Taxpayers expect their council to be filling potholes, not pay packets."