The MoD paper, the latest in a series of Whitehall reports assessing the impact of independence, casts doubt on Nationalist claims that an independent Scotland would inherit a share of UK armed forces personnel and equipment, then reconfigure existing bases to accommodate them.
It argues that an independent Scotland should not expect Scots servicemen and women to be transferred automatically from the UK military.
And in further extracts made public yesterday, it claims it would be costly and time-consuming to establish the combined army, navy and air force Scottish Defence Force from scratch.
The report will be unveiled by Defence Secretary Philip Hammond in Edinburgh tomorrow. The SNP said he should instead use the visit to apologise for defence cuts.
The report warns: "Re-designing a new force structure that worked coherently would be a substantial task.
"Adapting the functions of Scotland's defence footprint would result in a substantial burden on the public finances of an independent Scottish state during establishment, and duplication of costs thereafter for the essential services currently provided on a UK-wide basis.
"It is difficult to predict how long the establishment phase would last but given the complex, integrated nature of the UK Armed Forces ... this would not be an easy process."
It adds: "Even basic re-design of military bases is a costly undertaking requiring substantial investment to cater for different operational needs."
The SNP propose a force of 15,000 regular and 5000 reserve personnel. Faslane would be converted from a nuclear base to a "joint force HQ" and Scotland's main conventional naval port.
All existing military bases in Scotland would be retained, the policy states, with the air force operating out of Lossiemouth and Leuchars. Scotland's defence industries would be supported by new orders for frigates and submarines.
The SNP plans to spend £2.5 billion per year on defence - £1bn less than Scotland currently contributes to MoD coffers - but the party has never estimated possible start-up costs.
Questioning the plan, tomorrow's MoD report highlights the case of Lossiemouth, where three squadrons of Tornado fast jets are about to be replaced by three squadrons of Typhoons.
Noting that "fast jets are expensive," it adds: "It is not clear whether or not an independent Scottish state would be in a position to prioritise long-term retention of such assets given the high overheads."
The report says negotiations over assets such as bases and equipment in the event of a Yes vote next year would be difficult.
It says talks over transferring Scots personnel - whom it argues share "bonds of loyalty" with UK comrades - would prove even harder and present "an extremely difficult challenge to overcome".
The Whitehall analysis also dismisses SNP claims Scotland does not receive a fair share of defence spending, arguing Scotland benefits from "every single pound" of the MoD's £34bn budget. As part of the UK, it insists, Scotland is able to "project power" and take part in major humanitarian missions.
The SNP's defence spokesman Angus Robertson said: "When Philip Hammond visits Scotland, he should be apologising for the litany of closures, disproportionate cuts, capability gaps and broken promises. It is so embarrassing that to claim an independent Scotland can't do better and is an insult to common sense and international comparison."
He added: "There can be no doubt that with the power to make defence and security decisions in Scotland, for Scotland, we will do much better."