Alex Salmond yesterday complained to the Defence Secretary that basing Scottish infantry soldiers outside Scotland will undermine attempts to boost the population.
The First Minister yesterday wrote to Des Browne saying it is "regrettable", as it "seems destined to lose Scotland, through marriage and other reasons, many of its young men who we would have hoped would make their long-term future after service life in Scotland".
The SNP leader's concerns were dismissed by a Whitehall source as "the best demonstration we could have of somebody manufacturing a grievance".
The MoD responded that three battalions will be permanently based in Scotland - the Royal Scots Borderers, the Royal Highland Fusiliers and the Black Watch - while the Argyll and Sutherland Highlanders and The Highlanders will be based in Canterbury and Germany.
Mr Salmond was writing to the Defence Secretary to raise claims that have been made about breaking the "golden thread" linking former regiments to different recruiting regions of Scotland.
As first reported in The Herald, there is concern at senior Army levels that recruitment is already being harmed because soldiers will be attached to units wherever they are required, to maximise armed forces' flexibility.
The regiment campaign claims promises are being broken to retain former regimental names within the new, merged Royal Regiment of Scotland, to keep cap badges for the former regiments, continuing to base the soldiers in Scotland and supporting regimental museums.
Mr Salmond wrote: "If the undertakings are not being held to, and if the threads are being allowed to fray, then many people might feel that the decision to amalgamate the regiments was based on false promises".
A spokesman for the Ministry of Defence responded last night that the commitment to retain the golden thread remains in place.
"Nothing has changed and the Army works hard ensuring that the proud heritage of Scottish soldiering continues," he said.
"As part of that commitment, the Army retained regimental museums, home headquarters and hackles. The names of the antecedent regiments continue in the new batallion names and the Royal Regiment of Scotland continues to actively preserve links and battalion footprints with Scottish communities and regions."
It is claimed the basing of three Scottish battalions in Scotland offers more permanence than before.
A year after the Royal Regiment of Scotland was formed, the ministry spokesman added: "The Army has moved on and our busy Scots soldiers look to the future.
"They are proud to serve in their regiment and battalions, and wear their cap badge with pride. They are also taking advantage of the new and varied career opportunities that the new, more-flexible, regiment provides."
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