Local government minister Derek MacKay wrote to Fife and Moray councils saying they could not call a moratorium because it would cause "undue delay" to developments.
But the councils say they are being inundated by "opportunistic" planning applications and need time to consider the development ideas being put before them, and consult on new planning guidance for wind farms.
Local authorities in Scotland received 1,800 applications last year alone, the Daily Telegraph has reported.
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Moray Council said the request for a moratorium had received "significant support" from local people and described the response as a "bitter blow".
Mr Mackay's rejection came two months after he wrote to all councils instructing them to set up areas for building more turbines.
Mary Scanlon, Scottish Conservative energy spokesman, slammed the minister's decision.
She said: "When it comes to issues of renewable energy the SNP will do anything to force through its policies, completely ignoring the very legitimate concerns of local people."
Although Fife and Moray were the first to make written requests, Aberdeenshire has also called for a six-month halt after receiving 800 applications in only 14 months.
But a Scottish Government spokesman said ministers are considering more ways of helping councils deal with green energy planning applications.
"We do not believe that a moratorium on wind turbine applications is appropriate - it would simply cause undue delay and uncertainty for everyone involved in applications," he added.
(NE)
