The UK has moved to block Scotland taking part in a European Commission investigation into No 10 plans to subsidise a new nuclear plant in England.
A UK minister has warned his opposite number at Holyrood that any representation to Brussels on controversial plans to support a power station at Hinkley Point in Somerset would be viewed as a "hostile act".
In a potentially explosive row, Tory energy minister Michael Fallon is understood to have approached his SNP counterpart Fergus Ewing to "discourage" him from co-operating with European Commission (EC) investigators.
Mr Fallon's move came after the EC signalled that a deal with French firm EDF to build a new plant at Hinkley - designed British officials said to "keep the lights on" - may amount to illegal state aid.
The Scottish Government, which opposes nuclear energy, is understood to be concerned about the project, not least because it could pose competition to renewable exports from north of the Border.
Alex Salmond has now written to Prime Minister David Cameron accusing Mr Fallon to trying to silence Mr Ewing in a February phone call.
In a letter seen by The Herald, the First Minister said: "I am deeply concerned to learn that Mr Fallon made clear the purpose of his call was to discourage any direct representation from the Scottish Government to the EC concerning these issues.
"Mr Fallon stated such direct representation would be interpreted by the UK Government as a 'hostile act'.
"I would invite you to explain exactly what the UK Government would do if we choose to express our views to the Commission. At best, this could be interpreted as an inept attempt to stifle legitimate views from the Scottish Government. At worst, it is a direct threat with implied retribution."
A spokeswoman for the Department of Energy and Climate Change, stressed that Scotland "part of the UK member state in the EU and cannot act as a separate entity."
She added: "It would not be acceptable for one part of the same Member State to intervene against policy proposals from another."
Mr Fallon, she said, had simply told Mr Ewing his concerns should be raised directly with Whitehall, not Brussels.
The Hinkley Point row emerged just as Whitehall warned independence would put thousands of Scottish green power jobs at risk.
In its latest analysis paper, the UK Government warned the rest of the UK may choose to import low-carbon energy from Europe, not Scotland.
"Independence risks undermining the current basis for success of the low carbon sector in Scotland," it said. "The reality is that Scottish low carbon energy is unlikely to be able to rely on the current levels of financial support provided by all UK energy bill-payers. Scotland accounts for around 10% of UK electricity sales but gets 28% of the total paid by UK consumers to support renewables."