The row follows a decision to omit all planned Scottish offshore wind farms from a list of 10 "affordable" projects likely to receive UK Government support.
The developments could now miss out on a share of subsidies worth £4.5 billion.
SSE, the energy company behind one of the schemes, has already said it was disappointed by the announcement.
Energy Minister Fergus Ewing said that the decision had serious implications for Scotland's offshore wind industry and would increase uncertainty for developers and investors.
He also criticised the UK Government's priorities, saying: "They should be supporting the release of our green energy potential instead of being hell-bent on ploughing billions into nuclear power stations, which restricts the funds available to support renewables."
Liberal Democrat Energy Secretary Ed Davey has said that it would be a complete mistake to see the announcement of the 10 projects as somehow worrying for Scotland.
Schemes omitted from the list are eligible to apply for other subsidies or another round of the current funding in October next year.
Graham Lang of campaign group Scotland Against Spin, said: "The wind industry is hooked on public subsidy."