A job evaluation exercise, which will add an estimated £8m to Oxfordshire County Council's pay bill, is nearing completion.
The exercise, which has cost £200,000, began in 2001 and has affected more than 10,000 of the council's 18,272 employees.
About 3,000 staff will get a rise, while 6,000 will remain on the same pay. About 1,000 staff have been told their salaries will decrease, but they will get pay protection for three years.
But John Power, Labour county councillor for Oxford West, said: "That is a pay cut for some, however it is dressed up."
Thirty staff whose salaries were downgraded have appealed, while 70 others have asked for their posts to be reassessed. Staff have until the end of March to challenge their grades. In the majority of cases where changes are taking place, staff have been told they will go up or down a grade, worth about £2,000 a year.
Mark Fysh, the county's Unison branch secretary, said: "The union membership agreed to job evaluation on a 12-1 majority. If someone offers you £7m to make pay conditions better, you are not going to turn it down, but there is an appeal mechanism and we will continue to campaign for those staff who are losing out."
Sue Corrigan, head of personnel at County Hall, said: "Some people felt their jobs had been devalued and there was one resignation.
"Many staff, however, have felt their jobs have been recognised properly for the first time."
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