Fewer than half of local authorities will meet a deadline this month on equal pay structures for men and women, the Local Government Association says.
The agreement affects many low-paid workers
And some councils in England and Wales have done nothing to bring in the changes negotiated 10 years ago, the government has said.
The new structure is expected to add about 4% to wage bills and cost authorities £3bn in back-pay.
The LGA said a number of authorities are facing an "unmanageable burden".
Unions fear the pressure on councils will lead to thousands of job losses and mean higher council taxes.
An agreement was put in place ten years ago between trade unions and councils to equalise a pay gap between men and women doing similar unskilled or low-skilled jobs.
The Minister for Communities and Local Government, Phil Woolas, said some local authorities were far ahead of others in implementing the new structures.
"In some councils it's not a mess," he said.
"In some councils they've undertaken the job evaluation studies that have been required by the '97 agreement... to look at single status for blue and white collar staff as well as the crucial principle of equal pay for equal value.
"So some councils have done it, some have yet to do it and some haven't done anything."
Women workers who will benefit from the new pay structures include cleaners, classroom assistants and school dinner ladies.
Tina Kelly, a deputy cook at a primary school in Birmingham, said she and her colleagues have been waiting too long for a fair system.
"We've all been angry about it, because we've been just left at the bottom," she said.
Women around the country have been taking legal action to ensure they get the money they are owed in back-pay.
A European ruling means women are now entitled to up to six years' back pay, rather than two years as had been the case.
Bob Mather, deputy chief executive of Cumbria County Council, said council services may have to be cut to introduce the new pay structures.