The first minister should continue to investigate complaints about his own ministers' behaviour, the Welsh Government has said.
Carwyn Jones has rejected calls from a cross-party committee for the assembly's standards commissioner to examine claims against ministers.
He is concerned it could create confusion over the distinction between the assembly and the government.
AMs on the committee are unhappy with the response, BBC Wales understands.
Currently, complaints about assembly members are dealt with by the standards commissioner, Sir Roderick Evans.
But if the complaint is about an AM who is a minister carrying out their government duties, it is a matter for the first minister, who decides whether he or she breached their code of conduct.
He could refer the matter to an independent advisor, but the first minister would take any decision on punishment.
Calls for a more independent procedure have stretched back years.
A recent report by the standards committee called for a simplified complaints system for ministers, arguing that the ministerial code of conduct's requirement that the roles of minister and AMs are kept separate had the "potential for confusion".
The committee, chaired by Labour AM Jayne Bryant, accepts that it should be up to the first minister to decide who should be in their government.
But it said public confidence in the system could be improved if the commissioner examined complaints in the first instance, before reporting to the FM.
"If you have taken the important step to come forward to make a complaint about inappropriate behaviour, then you should not have to face the possibility of being told this was not the correct path and then being signposted to other channels," the committee argued.
"Complaints need to be dealt with from that initial point of contact," it added.
"We believe this will be simpler to understand and easier to access for the public."
But the Welsh Government said involving the standards commissioner - appointed by and accountable to the assembly - to investigate complaints about the behaviour of ministers "could create confusion in the minds of the public about where responsibility for ministerial conduct lies".
The independent advisor route has only been used once. James Hamilton cleared Carwyn Jones over whether he lied about past claims of a bullying culture in Welsh Government.
The government said that given the independent advisor had only looked at one case, "the committee's view that public confidence would be improved.... is not one that is shared by the First Minister".
The committee's report, which examined a range of issues about how the assembly deals with complaints, will be discussed by AMs on Wednesday.