Under the city council's equal pay shake-up, all staff were told that their existing pay would be protected for three years.
But hundreds of staff who are paid weekly have been left with lower wages than they had expected because they missed out on bonuses when off sick.
The new protected pay level is based on the average of bonus payments, shift payments and overtime payments actually received last year.
Unions are now set to take an offer from the council back to their members that still sees many miss out on money and are expected to recommend that they refuse the offer. That could lead to a further ballot on potential industrial action.
Stephen MacGregor, convener of the Unite union in Edinburgh, said: "The workforce feel conned by the way the council has implemented three-year pay protection.
"The mantra from senior managers in the council was 'there is no need to get involved in any dispute on pay protection because you do not lose one penny for three years'.
"There was no mention about how an average was being imposed for the first year of pay protection. It has been handled shambolically and the first time we were aware of it was when the first pay packet came out."
Kevin Duguid, a negotiator for Unison, said: "5, 10 or 15 may seem a small amount of money to some, but it is the weekly paid worker who is earning 200-300 that is losing it.
"Losing 10 a week is 520 a year, or over 1500 over the three-year course of pay protection. For families struggling to get by on the lowest wages on this authority, that is a large amount of money."
Council chiefs have said that paying the full bonus for all members of staff involved would cost an extra 750,000, including pension and national insurance contributions, for each of the next three years.
Councillor Phil Wheeler, the city's finance leader, said: "The administration is keen to see this matter resolved quickly and is hopeful that the continued dialogue with the trade unions will prove to be fruitful."
A city council spokeswoman said: "In an attempt to resolve this issue, we sent the trade unions our latest proposal. We then met with them on Friday to discuss a range of issues. At that meeting trade unions confirmed that they would have a ballot before submitting a formal response in January."