Nearly a quarter of council staff in Swindon face a pay cut as part of a job restructuring scheme costing £3.6m.
A similar number will see their wages increased as part of a review to ensure that all female staff are on equal pay with their male colleagues, the BBC reports.
Union Unison said each job should have been evaluated individually.
Spokesman Chris Howe said it was trying to work with the council about a year ago on how to achieve a fair pay system.
“When the council realised what a mess they were in historically, and how much it would potentially cost to get it absolutely right, they just walked away and invented their own pay system. That’s really what our complaints are [about],” he said.
“What should have happened is that every job should have been evaluated,” he added.
According to the BBC, letters describing the new structure will be sent out in January 2010, and those eligible for the pay increase will receive it from April 2010.
Those facing pay cuts will be cushioned from the immediate effect until April 2011 – at a cost to the council of £3.6m.
Deputy leader councillor Fionuala Foley said: “Some people will see a difference of a couple of hundred pounds and [for] some it’s quite a few thousand.
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“I’m not going to go into which types of jobs because most people don’t know yet. It’s all still being evaluated and the letters go out in January.
“It should be equal pay – more importantly, it should be a level playing field,” she added.
