Renewable energy opponents and experts said Audit Scotland had shone a spotlight on the flaws in government policy.
The report highlighted how the public sector had spent £209million on the sector since 2002-03 and funding would increase by £264million over the next two years.
The watchdog said progress was being made but added the number of jobs in the renewable sector was difficult to quantify and employment projections were “optimistic”.
Independent Highland campaigner Lyndsey Ward said: “The government is throwing figures up into the air fervently hoping that what comes down will be believed by the electorate.”
Stuart Young, of the Caithness Windfarm Information Forum, said: “The whole report is peppered with mays, mights and perhaps – there is so much uncertainty about the whole thing.”
Dr John Constable, director of the Renewable Energy Foundation, said the report showed the reluctance of the private sector to invest.
“The reasons for this are complex, but investors are certainly wondering whether the essential subsidies, which are overwhelmingly drawn from English and Welsh consumer bills, are sustainable in the longer term, and particularly in the event of independence,” he said.
Linda Holt, of Scotland Against Spin, said: “Audit Scotland’s gently devastating report shows that the game is up for the Scottish Government’s renewable energy policy.”
Scottish Tory energy spokesman Murdo Fraser said hundreds of windfarm applications will have to be approved if the government’s “ludicrous” plans are to be met.
Niall Stewart, chief executive of the industry body Scottish Renewables, said: “The report highlights the clear and strong energy policy from the Scottish Government, which has given the industry confidence to invest and build in Scotland.”