The Coalition's energy market reform plans represent "a huge risk to security of supply", Fergus Ewing said in a letter to UK Energy Secretary Ed Davey.
Mr Ewing said: "We have examined the UK Government's proposals carefully, discussing them in detail with the industry and other stakeholders.
"I believe beyond doubt that the current proposals risk failing Scotland and the UK in a number of vital areas, and present a huge risk to UK security of supply as well as to investor confidence and our low-carbon ambitions."
He said the Scottish Government would not support an outcome which sacrifices renewable ambitions in favour of "discredited, expensive and imported" nuclear technology.
"Nor should thermal generation in Scotland - vital to maintaining grid stability here, and to providing security of supply across the UK - be placed at risk through a failure to take Scottish issues properly into account," he said.
"Both Ofgem and National Grid have expressed deep concern regarding the risks that the UK faces both this winter and in the years ahead due to tightening capacity margins. It would be extremely unwise to ignore the vital and combined contribution of Scotland's renewable and thermal generation to keeping the lights on across the UK.
"Unless serious and considered steps are taken to address these matters, and which supports investment in thermal generation across the whole of the UK, then the threat of blackouts will crystallise rapidly."
He went on to warn that any failure to secure a proper margin of capacity over peak demand would "inevitably" see further price rises on energy bills, which he blamed on UK energy policy failure over the past decade.
"We now know that the UK Government has also proposed a last-ditch amendment to the Energy Bill, which will allow UK ministers to close the Renewables Obligation in Scotland. I find it extraordinary that the UK Government has chosen to act in this way, and to strip Scottish Ministers and the Scottish Parliament of their powers and discretion in an area of such vital importance," he said.
"The UK Government has produced this amendment with no consultation or explanation. We are deeply concerned about this summary removal of the Scottish Government's discretion in an area of such vital importance to our people and economy.
"As a matter of urgency the UK Government must provide a detailed justification for its action."