The basic salary of councillors will rise in 14 of Wales' 22 local authorities next year.
Members of the other eight councils will see their basic pay cut.
The Independent Remuneration Panel for Wales used new powers to tell councils what to pay their members.
The Welsh Local Government Association (WLGA) said it would mean a "significant" cut for some councillors and a pay rise for others at a time when council workers' wages are frozen.
Next year the basic salary for councillors will fall from a maximum of £13,868 to a mandatory £13,175. At present, eight councils pay more.
The changes will also affect what councils pay their leaders and other post holders. The leaders of the three biggest councils - Cardiff, Rhondda Cynon Taf and Swansea - will get £52,700. Smaller councils will pay £47,500 or £42,300.
The panel's chairman, Richard Penn, said it had been "very mindful" of the economic climate when making its decision, adding: "We have carefully considered the likely financial impact of prescription on local authorities."
"We recognise that in the short term our approach of prescribing payments could result in annual savings for some local authorities and additional costs for others," he said.
"However, we are making this change in response to the view consistently expressed to us by councillors across Wales that the setting of allowances should be taken out of the out of the political arena and thereby avoid a 'race to the bottom'."
He said the panel's annual report created a "fair, affordable and consistent framework".
The WLGA said it had raised its concerns with the panel about some councillors getting more at a time of local authority pay freezes.
A spokeswoman said: "Whilst the panel has responded to some of our concerns, we are disappointed as the report undermines some of the good work and standards the panel has previously set and places constraints on councillors and councils' future governance arrangements.
"The report limits the number of senior salaries that can be paid from next year, which means councils will have to either reduce the number of senior posts, thereby placing additional burdens on fewer individuals for less pay, or expect some councillors to take on key roles without any financial recognition."