Labour said that Scottish ministers missed opportunities to raise concerns about rising prices in correspondence with the energy giants over two and a half years, according to documents obtained under Freedom of Information rules.
Mr Miliband said: "It's becoming clear that, like David Cameron, Alex Salmond is happy to stand up for the Big Six energy bosses, rather than hard-pressed families across Scotland. Alex Salmond's plans for separation will mean higher energy bills for Scottish families and businesses."
But a spokesman for the First Minister rejected what he said was a "ridiculous and false" claim, and said ministers had discussed the issue with one firm only last month.
The attack comes ahead of a Commons vote today on Labour's call for an energy price freeze. Scottish energy minister Fergus Ewing has described the policy as "unworkable".
The Conservatives have also opposed the plan on the same grounds. Last week SSE announced it was freezing prices, becoming the first of the Big Six to do so. Making its announcement, the energy firm credited the Coalition's cut in green taxes for the move.
A spokesman for the First Minister last night said: "Scottish Government Ministers have regularly raised the issues of energy bills and fuel poverty over the last few years.
"Most recently the Deputy First Minister raised these issues at a meeting with Eon last month. Labour need to wake up to the fact that the Scottish Government's plans to cut energy bills by £70 a year on an on-going basis is far better for household budgets that their plans for a temporary freeze."