The claim is made in a paper to be launched by Defence Secretary Philip Hammond in Edinburgh next week.
An extract states: "An independent Scottish state could not simply co-opt existing units that are primarily recruited or based in Scotland, as these are an integral part of the UK Armed Forces.
"Personnel might very well not wish to leave the UK Armed Forces to join much smaller forces, not least because of strong bonds of loyalty."
However, the Scottish Government say that an independent Scotland will have first-class conventional forces and that Scotland stands to inherit a fair share of existing UK defence assets.
And SNP defence spokesman Angus Robertson MP wants Mr Hammond to apologise for UK cuts in the armed forces when he visits Scotland to launch the paper next week.
Mr Robertson said: "After the years of broken promises from Westminster Governments, and when soldiers serving in these regiments are being handed P45s by Phillip Hammond, the Defence Secretary's words will be particularly hollow.
"If there is one area which shows that Scotland has to be better at making decisions for ourselves than Westminster is, it is the lamentable record of the Ministry of Defence in Scotland.
"Three airbases are being reduced to one. Uniquely as an armed maritime nation in northern Europe we have no maritime patrol aircraft and have no ocean capable conventional vessels based in Scotland.
"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 is an insult to common sense and international comparison."