The detailed study, published today, argues that Scottish-generated renewable energy could help keep the lights on and prices down across the UK in the event of a Yes vote.
But it says an independent Scotland would require "a far greater degree of oversight" of a continuing UK-wide energy market because current Coalition Government policies risk causing power shortages.
The paper - released as a key North Sea employer, engineering giant AMEC, became the latest company to voice concerns about a Yes vote - reignited the row over whether independence would help or hinder the country's growing green power industry.
It is expected to dominate the independence debate this week as the UK Government is in the next few days expected to publish its latest Scotland Analysis paper on the consequences of a Yes vote on the energy market.
The paper prepared by the Department of Energy and Climate Change is expected to warn the Scottish Government's drive for wind power would lead to soaring bills and blackouts in an independent Scotland.
The Scottish Government report points out that England imported almost as much electricity from Scotland as it did from mainland Europe in 2012.
It argues that, in the event of independence, a UK-wide energy market should be maintained with Scottish renewable energy playing a central role.
But it accuses the UK Government of failing to protect "security of supply" by ensuring the country has enough generating capacity to meet demand.
It blames ministers for failing to do enough to encourage investment in renewables and focusing too heavily on new nuclear power stations.
It also warns of Britain's energy margin - the difference between supply and demand - falling to just 2% over the next few years.
The report concludes: "There is common interest in sharing energy resources across these islands.
"However, as a substantial supplier to the rest of the UK, an independent Scotland will require a far greater degree of oversight of the market arrangements for energy and firmer safeguards over Scottish energy security.
"The policies of the UK Government have brought us to the point where the risk of black-outs is the highest for a generation."
The report says a formal "energy partnership," to form joint policy with the rest of the UK, would safeguard an independent Scotland's power supplies.
SNP Energy Minister Fergus Ewing accused the UK Government of harming investment in green power by sending "mixed messages" to the industry.
He added: "It's time for the UK to sort out their energy policy, stop driving away investment and instead start addressing their security of supply problems instead of making them worse."
Labour's shadow energy minister Tom Greatrex said: "The Nationalist energy spokesman seems not to understand that tightening of capacity margins across all of the UK will not be solved through intermittent wind generation from here in Scotland.
"The margins tighten when the wind isn't blowing, and with an increasingly imbalanced energy mix in Scotland, that is more of a future risk for us than the rest of the UK if we walk away from the UK's single energy market."
The row came as Samir Brikho, the chief executive of global engineering firm AMEC, said: "I believe in the UK - that being together is a better outcome for both the Scots and the English."
He said he believed that North Sea production could remain "stable" in the coming years but warned uncertainty created by independence might jeopardise the investment that would be required to extract the oil.
AMEC, which employs 4500 people in the North Sea industry, joined Shell and BP in raising concerns about independence.