The paper titled "UK energy policy and Scotland's contribution to security of supply" said that the UK government's uncertainty on securing energy supply is risking higher bills and blackouts.
It added that an independent Scotland would be able to help keep the lights on, but would demand to have greater influence on UK energy policy as well as help Westminster meet its 2020 green energy targets.
"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.
"Scotland offers safe and secure supplies of electricity and gas and can assist the rest of the UK in meeting its renewable energy targets."
Scottish energy minister Fergus Ewing added: "The more capacity you have available — especially from lower marginal cost generation such as renewables — the lower wholesale energy prices will be, again highlighting the value of Scottish generation to every household across these islands."
In March, Scotland-based SSE, one of the Big Six energy suppliers, said should the outcome of the referendum result in an independent Scotland, negotiations would follow with the likely result being a single British energy market.
In February, SSE withdrew plans to construct two Scottish wind farms with a combined capacity of 117MW because they were deemed to be no longer "financially viable".
The Scottish government's new report comes just days before the UK's Department for Energy and Climate Change (Decc) is to release its own paper on the consequences on the energy market of a Yes vote in September's referendum.
Decc is expected to say the Scottish government's drive for wind power generation could lead to soaring bills in Scotland as consumers will need to pay for increases in capacity.
Energy secretary Ed Davey told the Scottish Renewables annual conference in Edinburgh last month that Scotland would have to compete with other renewable energy exporters to win UK contracts.