A letter published this month in the Tenerife News included a request from Simon Montague, the embassy's director of communications, in which he urged the title to print a Home Office press release about the "challenges" if Scotland left the UK.
The SNP claimed the letter showed the Foreign Office (FCO) was trying to whip up hostility to independence overseas, despite David Cameron's insistence that September's decision is purely "a debate between Scots", the argument he has used for refusing to debate with Alex Salmond.
Westminster sources said the SNP was talking "nonsense", and pointed out that the FCO routinely helps Scottish ministers with overseas visits on which they promote independence.
The embassy press release included comments from Mark Harper - who yesterday resigned as Immigration Minister after it was discovered he had unwittingly employed an illegal immigrant as his cleaner - about one of Westminster's "Scotland Analysis" papers on border control and citizenship.
Montague's preamble, which the English-language paper printed in full, suggested the embassy was systematically asking Spanish papers to report the pitfalls of Scotland leaving the UK.
It said: "Dear Editor, Given the likely interest among your British resident audiences - whether Scottish or otherwise - I am forwarding you a press release issued by the Home Office today.
"The paper … explores the challenges which an independent Scottish could face in assuming control of its borders and considers the difficult choices that the people in Scotland would have to face on issues such as citizenship and nationality.
"It will be a choice between the continuity and security of being part of the UK or the uncertainty and risk of leaving it."
The Sunday Herald revealed last month that a FCO unit set up to promote the Scottish Government's interests was also being used against it.
The Devolution Unit, which was set up in late 2012 to deliver the "utmost co-operation" overseas, now handles feedback from foreign governments on the prospect of a Yes vote in September.
It helps Westminster to have allies who can raise questions about an independent Scotland's membership of international bodies such as Nato, the United Nations and the European Union.
Alex Salmond has already accused Spanish prime minister Mariano Rajoy - who is already wary of Catalonia pushing for independence - of "plotting" with Cameron to raise questions about Scottish independence.
Angus Robertson, the SNP's Westminster leader, said: "Our embassies should be promoting our interests abroad but instead, under instruction from the UK Government, they are actively seeking to undermine Scotland.
"This is exactly the kind of behaviour that demonstrates why Scotland must be able to represent our own interests as an independent nation on the world stage.
"That the UK Government is going to these lengths to scaremonger on independence is another indication of how desperate and worried the No campaign has become."
A UK Government spokesman said: "The letter in question simply points out the UK Government has published an analysis paper, nothing more. It is information for people living abroad.
"The UK's embassies work hard for our country's interests, including promoting Scottish trade and protecting Scottish citizens.
"The FCO frequently facilitates overseas visits by Scottish Government ministers where they can promote their policy of independence should they choose."