Edinburgh City Council has been branded shambolic, after a report revealed that £275,000 has been unaccounted for.
The problem emerged when auditors Deloitte reviewed repair work done on a tenement, which was organised by the council and amounted to more than £1m.
There has also been criticism of the scheme replacing the statutory notice system, which has been at the centre of a multi-million pound scandal.
The council said it was not able to comment on individual cases.
The statutory repair system had been in place for decades in Edinburgh and allowed the council to force homeowners to make repairs to shared tenements when they could not reach agreement themselves.
However, the value of statutory notices issued by council surveyors increased dramatically, from £9.2m in 2005 to more than £30m in 2010. Some homeowners complained about overcharging, unnecessary and poor quality work.
The system was suspended in 2011, amid claims that bribes had been offered by contractors, and of cosy relationships between contractors and council officials.
No charges were ever brought in the department, which dealt with private homeowners, although two council officials were convicted of bribery in the Property Care department.
Twelve years on and the cracks are still on show at Jeremy Pascoe's tenement flat in Leith.
In 2003, Mr Pascoe and his 15 neighbours needed to get their stonework repaired.
The council took on the responsibility of organising the work.
However, according to Mr Pascoe, about three times as much stonework was done as was recommended in the original survey, as well as the demolition and rebuilding of several chimneys.
The homeowner had to use Freedom of Information law to get hold of the full review of his bill.
He said: "We had a Historic Scotland grant on this building, which I think is right because it's an important building and it should be repaired properly. The grant was around £300,000."
The Deloitte report said of the case: "Deloitte have spoken to Historic Scotland, who confirmed that the amount had been agreed and that £276,000 has been paid. However City of Edinburgh finance team have confirmed that they cannot find evidence of this payment."
Mr Pascoe said: "It's just an example of the poor management of the project and their poor record keeping throughout.
"I've been treated appallingly. It's 12 years of my life and, I think, thousands of hours of my time I have spent chasing this. And I'm quite convinced that if I hadn't done so we would've been billed for far more."
He added: "Our works vastly grew in scope, with probably about £500,000 worth of work done which was not on the notice - most of which we've not been billed for, in fairness.
"The council has written off about £500,000 that has been paid to contractors. That's not the final sum because we are not accepting the bill that's being presented to us. And the council will have their own internal costs.
"It's very poor value for the City of Edinburgh council tax payers - they're picking up a bill of, depending on what you include, between half a million and £1m for this building alone."
Almost half of Edinburgh's properties in the capital are shared tenements.
Councillor Cameron Rose, who has been putting pressure on the council to deal fairly with owners, said the missing funds "beggared belief".
"Doesn't that just show the shambles surrounding the whole scandal?" he said.
"We've got an amount of money so large and yet no record of where it is. We're talking about hundreds of thousands of pounds here.
"And that just undermines any confidence that people have that they've been getting a fair deal now, when a bill arrives on their doorstep."
The repairs system was stopped four years ago, except for emergencies. But it is due to start up again in the New Year.
Architect James Simpson said he does not think appropriate safeguards are in place.
"The basic problem was that the council got involved in all sorts of matters in which it shouldn't have got involved," he said. "That, I think, led to huge mismanagement.
"I don't think anybody wants that to happen again. And the best way of avoiding that is for the council to step back, not get directly involved, but co-operate with others - including perhaps the Edinburgh Architects Association and the Royal Institute of Chartered Surveyors - with a view to setting out a Code of Good Practice, and publicising it to encourage and educate property owners in how to manage and maintain their communal property."
David Gibbon, a chartered building surveyor specialising in conservation, told the BBC he "couldn't accept the idea of the council doing this all over again".
"They haven't even cleared up the mess they made the first time," he said.
A council spokesperson said: "The council would like to stress that in light of the issues that have arisen out of the former statutory repairs service, we are taking an independent, objective and consistent approach to our billing processes.
"We have now reviewed our debt policy to make it more flexible, allowing repayments to be made over a more manageable period of time."