Industry representative body RenewableNI said that the work was “not fit for purpose” and should be disregarded.
But the Audit Office has “strongly refuted” the assertion.
RenewableNI took issue with the report published in October.
It focused on stand-alone single wind turbines, not big wind farms.
The report used the example of a turbine that could earn £95,000 per year in subsidies and pay back the £300,000 build cost in four years, enjoying a further 16 years of payments.
There are 1,200 such stand-alone turbines in Northern Ireland.
The Audit Office said the payments, raised from a levy on customers’ electricity bills, were “excessive”.
RenewableNI said the figures in the Audit Office report were based on a single turbine that was not connected to the electricity grid.
It disputed the cost assumptions and said its members, which are delivering such projects, did not recognise the figures.
image captionFormer Green Party leader Steven Agnew took over as head of RenewableNI last yearimage copyrightPA
“From initial investment, development and generation costs to ongoing maintenance, insurance and operating costs, the Audit Office has got it wrong on all counts,” said spokesman Steven Agnew.
“In doing so (they) have undermined the significant contribution of the small scale renewables sector to the economy and the environment.”
He said they had not only lodged a formal complaint with the Audit Office under its grievance procedure but commissioned accountants to produce an independent audit.
RenewableNI said the cost of buying and installing a turbine was typically at least £600,000, twice what the Audit Office had suggested.
The Audit Office confirmed the complaint and said it had offered to meet RenewableNI to discuss their concerns.
It said due to the absence of official data on rates of return for turbines from both the Department for the Economy and Office of Gas and Electricity Market (OFGEM), the body which administers the scheme, it had done its own calculations.
“We consider that our calculations are a reasonable estimate of an average rate of return,” the Audit Office said.
“As with all of our reports, this report is evidentially based and its accuracy was agreed with the Department for the Economy and the Utility Regulator in advance of publication.”
RenewableNI said it understood that BBC Spotlight was working on a programme based on the findings of the Audit Office report.
It said it had made the production team aware of its concerns over the accuracy of the figures in it.
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