Pembrokeshire's council leader claims Labour ministers are "targeting" independent-run authorities for criticism ahead of local elections.
John Davies, who is also leader of the Welsh Local Government Association, is embroiled in a row with the education minister over child protection.
Mr Davies has been criticised over his response to two critical inspection reports.
The Welsh Government declined to comment on his remarks.
Referring to a number of critical comments by ministers about certain councils recently, Mr Davies told BBC Wales: "A large number of people are now asking this morning what is behind this.
"We are an independent-run council in Pembrokeshire, as Blaenau Gwent is an Independent-run council, and others, and these are the councils that are being targeted at the moment."
In July, Blaenau Gwent local education authority became the first in Wales to go into special measures after a report found "systemic" management failures.
Mr Davies said the current fraught relations between councils and ministers could have a damaging effect on services.
"There has been a significant deterioration in relations between local authorities and the Welsh Government in recent months, which is sad," he said.
"The ministers have changed recently, there are new faces, and there is an unfortunate attitude towards sustaining the kind of relationship needed for good government in Wales."
All local councillors in Wales face an election in May 2012.
Senior Pembrokeshire council figures were accused of making misleading statements in the wake of two inspection reports criticising the county's education and safeguarding services.
Education services for children and young people were judged "unsatisfactory" by schools inspectorate Estyn, which said the "policies and systems for safeguarding children and young people are not fit for purpose".
A report exposing the council's failings over child abuse allegations was described as "deeply disturbing" by Wales' children's commissioner.
Mr Davies said at the time that he wanted to assure parents staff were working tirelessly to ensure children were as safe as possible.
The Welsh Government accused Mr Davies on Wednesday of trying to play down the reports' seriousness in some media interviews.
'Lack of rigour'
The criticism was contained in a letter from Education Minister Leighton Andrews and Social Services Minister Gwenda Thomas.
"Your authority has demonstrated a lack of rigour and urgency in undertaking this work, as evidenced by the fact that it was not until the inspectors started to point out some of the issues that your authority even realised that there was a problem," wrote the ministers.
"Even then, in one case inspectors had to refer back to your officers four times before all the action that was needed was taken."
Mr Davies said some comments in the letter were factually inaccurate.