Ahead of this week's Nato summit in Wales, the former diplomat and Black Watch officer said: "No time in the last 30 years has there been more extremely difficult politics. We're struggling to cope with events in Afghanistan, Russia is creating uncertainty in eastern Ukraine, Iraq is collapsing and extremists have taken over the Libyan capital.
"It is a time when smaller countries are experiencing difficulties and we have to come together to work together. Frankly, Britain, as a medium-sized power, still has influence in the world. This is a very dangerous time and a risky time to be damaging the UK's defences through Scottish separation."
Asked about the SNP Government's desire for an independent Scotland to rid itself of nuclear weapons yet become a member of the nuclear-based alliance that is Nato, Mr Stewart, who represents Penrith and the Border, said: "The US and other Nato members have made clear they would be very disappointed. They would do their best to accommodate Scotland but it would very much far from ideal."
The Scot added: "Scottish independence would be a source of instability and complexity we don't need at a very unstable and complex time."
But Angus Robertson, the Nationalists' defence spokesman, hit back, saying: "The ridiculous scaremongering of the No campaign - in the same vein as Lord George Robertson saying an independent Scotland would be 'cataclysmic' for the entire world - is driving more previously No voters and undecided people into the Yes camp. The approach of the Tory-led No campaign is inept, which I suppose we should welcome."
He added: "Nato's own stated intention is for membership to be open to all European democracies that meet the membership criteria and given that Scotland occupies a key strategic location in the North Atlantic, our continued membership will clearly be in the strong interests of the rest of the alliance."
As world leaders gather for the two-day summit at Newport in south Wales - said to be the largest security operation ever mounted in the UK - the SNP defence policy has already been attacked by a former Nato chief.
General Sir Richard Shirreff, who recently stood down as Nato's Deputy Supreme Allied Commander in Europe, branded the Scottish Government's defence proposals for an independent Scotland "amateurish and unrealistic".
He claimed there was "no certainty" about an independent Scotland, which would be seeking to rid itself of Trident nuclear weapons by 2021, becoming a member of Nato.
The SNP, who have made removal of nuclear weapons a clear red line in any post-independence talks, responded with Mr Robertson noting that the people who had a "dangerous and amateurish" defence policy were those who had sent troops to an illegal war in Iraq and who were wasting tens of billions of pounds on Trident i.e. the Coalition.
Alex Salmond, the First Minister, and his colleagues argue that because of Scotland's important strategic position in relation to the Arctic to the north and the Atlantic Ocean to the west, an independent Scotland would be a key partner in Nato's air and naval policing arrangements for northern Europe.
They also point out how other similar sized countries like Norway and Denmark play key roles in alliance operations and they are among 20 of Nato's 28 members, which neither possess nor host nuclear weapons.
But Gen Shirreff poured cold water on any idea of a swift entry into Nato for an independent Scotland, insisting: "It is highly unlikely Nato will agree to any further expansion while the promise of Nato membership made to Ukraine and Georgia in 2008 is still on the table."