The three remaining members of the Scottish Local Authorities Remuneration Committee (SLARC), set up to scrutinise councillors' pay and expenses, have quit amid allegations of ministerial neglect.
One of them, Jack Wilson, said Mackay should be "held to account" for his "inappropriate" action.
SLARC was set up in 2005 by Holyrood to advise ministers on the remuneration of councillors.
The statutory committee played a central role in investigating the extra payments councillors pocketed for sitting on arms-length external organisations. Such payments were rife in Glasgow, and the system was dismantled following a hard-hitting report by SLARC.
As well as making proposals to the Scottish Government, the committee monitors councils and has been a point of contact for local authorities on expenses.
However, SLARC's work now appears to be at an end – Mackay, a former councillor himself, has wound down the respected body.
Vacancies have not been filled and SLARC has been left with only three members: the convener, Ian Livingstone; Mark Irvine, a consultant; and Wilson, an accountant.
The terms of Irvine and Wilson were due to end next month, but the pair have resigned due to the treatment of the committee.
In his letter to the minister, Wilson said: "Since you took up responsibility for the committee I have been unimpressed with your performance in your dealings with the committee.
"You have shown no real interest or respect or consideration for the committee or its chairman as it has taken until last week even to get a meeting with you."
Wilson said SLARC was an independent committee set up by Parliament, not the Government: "I believe that it is the responsibility of ministers to respect and protect the decisions of Parliament and you have clearly not done this on this occasion."
He accused Mackay of following a "personal agenda", adding: "I think you have to be held to account for this inappropriate action."
In his resignation letter to the Local Government Minister, Irvine said: "I am very disappointed in your lack of support for SLARC and, in particular, for the committee's robust and independent role on remuneration issues."
Livingstone, whose term as chairman was due to end next year, confirmed he had also resigned.
He told the Sunday Herald: "It is a matter of regret that the monitoring and communications roles will not be continuing."
Labour MSP Sarah Boyack said: "The SNP has yet again shown its contempt for Parliament and local government - an independent statutory committee set up by Parliament has been left to wither and die without any reference to Parliament. I will be raising this in Parliament on Thursday when we debate local government finance."
Scottish Liberal Democrat leader Willie Rennie MSP said: "Derek Mackay must come before parliament and explain why the highly praised and independent SLARC has declined into a phantom committee under his watch."
A Scottish Government spokesperson said: "There are currently no significant issues about councillors' pay on which ministers require advice from SLARC - We therefore intend to stand SLARC down until such a time as we require it to undertake further review work."