One Flintshire worker says he faces a 25% pay cut under the deal
Some workers at a north east Wales council say they could lose up to a quarter of their wages.
It follows moves by Flintshire council to implement an agreement on equal pay, signed by councils over a decade ago.
One member of staff said he has received a letter telling him his salary will drop by £5,000 a year.
The council said it has written to 6,000 staff confirming new pay agreements, and insisted that around half will see their wage increase.
But a member of staff working in leisure services said the decision had been a bombshell.
"I'm pig sick, and other members of the department are distraught," said the worker, who asked not to be named.
"People have been finding out about it during the day. Everyone is gutted."
The Flintshire employee said he had been told that his pay would be cut by 25% by the middle of 2011.
"I was looking for somewhere to rent to live in the area, but now I don't know if I can afford to.
"It's a massive cut. It means I won't be able to do anything, I won't have the money."
The Single Status Agreement was signed in 1997 by all UK councils, in an attempt to end unequal pay in local government, especially differences in manual and white-collar pay between men and women.
EQUAL PAY TIMELINE
From the late 1960s, bonuses were introduced in jobs where productivity could be easily measured - often full-time manual jobs usually done by men
Manual jobs often done by women, such as care work, usually did not include a bonus
A 1997 agreement led to a single pay structure for manual and white collar staff - all local authorities agreed to carry out job evaluations to ensure equal pay
Progress was slow but in 2004, a timetable was put in place to complete job evaluations and pay structures
Most Welsh local authorities have now completed their job evaluations, and are drawing up pay and grading structures which must be agreed with trade unions
Source: Welsh Local Government Association
Flintshire council chief executive Colin Everett confirmed that letters were being sent out to around 6,000 of the authority's 9,000 staff, confirming new grades and pay under the single status agreement.
Mr Everett said around half of those affected by the changes will see their pay increase, and three-quarters will also see their maximum pay grade point rise.
However, he admitted that it did mean some council employees would be adversely affected.
"There are a lot of positive changes, but clearly there's mixed emotions," he said.
"What we have agreed is to protect the pay of anyone whose salary is due to go down for two years.
"The over-riding message is we understand, we empathise and we will be spending a lot of time talking to our staff over the coming weeks and months."
He said all staff would have a right to appeal against any changes.
There will also be a ballot of union members in the authority in November to decided whether the agreement is acceptable.