Only eight out of 53 outstanding applications before Holyrood ministers are known to have been granted a generating licence by the watchdog body. Another site has an exemption from the usual requirement to gain a licence.
The 44 remaining projects could potentially fall foul of a planning ruling published last week, anti-wind farm campaigners believe.
In a Court of Session ruling Lady Clark of Calton overturned permission previously granted in April for the 370 megawatt Viking wind farm in Shetland.
She said the scheme needed to have a generating licence before it could be given the go-ahead.
The government has said it will appeal against the ruling.
Anti-wind farm campaigners, however, insist the ruling could be used to block other applications with no generating licence.
It emerged yesterday that the Scottish Borders Council had written to the Scottish Government, demanding that an application for a RWE Npower Renewables wind farm at Rowantree, near Oxton, be refused on the grounds it has no generating licence. Council lawyers believe the Shetland case sets a legal precedent.
Graham Lang, chairman of national anti-wind farm alliance Scotland Against Spin, said there was "little doubt" that other local authorities would raise similar objections.
But a Scottish Government spokesman said licensing arrangements were being studied.
He said: "The 53 outstanding onshore wind farm applications held by Scottish ministers includes 14 that are at initial application stage and not yet formally submitted.
"Of the remaining 39 active wind farm applications we know of eight which have an Ofgem generating licence, and one which has an exemption.
"We are in the process of liaising with Ofgem to establish the licence status of the remaining 31."
Major wind farm development of more than 50 megawatts require approval by ministers. Since 2007 the Scottish government has granted permission for 32 such projects.
However a further 53 are in the pipeline, 14 of which are at an early stage.
Onshore wind farms account for the vast bulk of renewable energy generated in Scotland, which currently amounts to the equivalent of 40% of the country's power needs.
The Scottish Government has set a target of generating the equivalent of 100% of Scotland's energy needs from green sources.