Labour's Lord West of Spithead also claimed Scotland would suffer a "huge economic impact" from defence firms moving south.
The ex-security and counter terrorism minister's comments came at question time in the Lords ahead of the September referendum on independence.
Lord West said: "It's quite clear that the defence of our islands will be considerably weakened if the Scots vote for separation.
"There will also be a huge economic impact by defence firms inevitably moving south of the border because there will be almost no orders for defence equipment in Scotland."
Treasury spokesman Lord Newby said this was one of the "many inevitable consequences" were independence to happen.
He told peers: "Independence isn't for Christmas. It's a long time business. Once you've done this you can't reverse it."
Lord Newby said there was increasing evidence from the business community that they believed their "involvement in the Scottish economy would be reduced" if independence went ahead.
He said BP was just the latest major firm to "question their long term involvement in the Scottish economy if Scotland became independent".
Liberal Democrat Lord Razzall asked if ministers believed Scottish first minister Alex Salmond was behind "the suggestion RBS would re-locate to England in the event of independence".
He said that if the last "bail-out" had occurred in an independent Scotland it would have bankrupted the Scottish economy.
Lord Newby said this "may be right". An independent Scotland would have banking assets equivalent to 1,254% of the Scottish GDP - more than Ireland, Iceland and Cyprus "when they ran into banking difficulties".
Labour former minister Lord Foulkes of Cumnock recalled to laughter from all sides that Mr Salmond used to be an economist with RBS, adding: "Doesn't that say a lot."
He said economic growth in Scotland for the third quarter of last year was much the same as in England, which showed that "devolution is working and that Scotland is getting the best of both worlds".
Lord Newby said he agreed with that.
SNP Westminster leader and defence spokesman Angus Robertson said: "Successive Westminster governments have overseen the destruction of the Scottish regiments, and contributed to a massive multibillion-pound defence underspend in Scotland compared to the rest of the UK.
"Scotland has no major conventional surface vessels based there, no maritime patrol aircraft, and of the promised 7,000 soldiers that were supposed to return from Germany to Scotland, not a single one has.
"The Secretary of State for Defence (Philip Hammond) recently revealed his reliance on Twitter for intelligence when Russian forces entered Scottish waters. Unionists are hardly in a position to lecture Scots about capabilities.
"The choice is clear - Scotland needs a Yes vote on September 18 2014 so that we can secure better defence policy decisions for our country."