Craig Murray, former British Ambassador to Uzbekistan, claimed the intelligence organisation had undercover officers in Scotland who wanted to smear the SNP.
An office belonging to the Conservative party was branded with the word "scum", a swastika sign and a letter "Q" in what appears to be spray paint.
A "Q" was also spray painted onto the a Labour party office. The "Q" is meant to represent the word "quisling", or traitor.
But Craig Murray, a former British Ambassador to Uzbekistan from August 2002 to October 2004, has claimed that the MI5 were responsible for the actions. He accused the intelligence organisation of having officers within the SNP.
"A sweeping SNP victory on May 7 is considered enough of a threat to the United Kingdom for the security services to use up some assets," Murray wrote on his website.
"Long term sleepers within the SNP will now be activated, so expect to find one or two such events traced to apparent bona fide SNP members".
Murray, who was sacked from his role as ambassador by Tony Blair's government, said these alleged intelligence officers would attempt to provoke nationalists into carrying out "vandalism or violence".
He wrote: "A major thrust will be agent provocateur activity. Security service agents within the SNP will be trying to initiate and to egg on [a reference to Scottish Labour leader Jim Murphy getting egged during the independence referendum campaign] impressionable members to vandalism or violence.
"Be very, very wary of such people and do not be tempted".
Murray wanted to stand in the general election as a candidate for the SNP but was deemed to have a "lack of commitment to party discipline" after he went through a vetting process by the party.
In September last year – during the campaign for the Scottish independence referendum – research for BuzzFeed News by polling firm YouGov found that 26% of Scots thought it was "probably true" that security services were trying to stop Scottish independence.
Officials believe the graffiti was spray painted either on Friday night or early on Saturday.
"Once again we see the ugly side of nationalism on display," Thompson told STV.
"People should engage in healthy democratic debate but attempts like this to try and intimidate and bully political opponents are utterly disgusting."
He added: "I do feel a bit intimidated, seeing it gives you a horrible feeling that you're being targeted."
A spokesperson for the Home Office said it would comment on security matters. The SNP did not respond for a request for comment by the time of publication.
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