Kenny MacAskill, 62, believes "dark forces" were at work during the trial of Mr Salmond, who served as Scotland's first minister between 2007 and 2014.
Mr Salmond, 65, was found not guilty on 12 charges of sexual assault at the High Court in Edinburgh last month.
Mr MacAskill, who served as justice secretary under Mr Salmond's SNP government between 2007 and 2014, hit out at prosecutors for pursuing charges which he branded 'utter bunkum' and 'pretty flimsy'.
He believes there was an "orchestrated campaign" by senior people in the Scottish Government and SNP who wanted Mr Salmond's head "on a platter".
He also accused police of mounting an inquiry of "gargantuan proportions" while complaining about tight budgets.
The East Lothian SNP MP also claimed the downfall of Mr Salmond's lead lawyer, Gordon Jackson QC, may have been part of a wider conspiracy against the former first minister.
Mr Jackson resigned as dean of the Faculty of Advocates barely a week after the trial when a video emerged of him reportedly naming two of Mr Salmond's accusers on a train, despite a court order granting them anonymity for life.
Writing in the new issue of the Scottish Left Review, Mr MacAskill said what happened to the QC seemed "more than accidental" and his "real crime" was representing Mr Salmond.
Mr MacAskill said: "It certainly seems that, as well as the poison and prejudice of a few, there were other 'dark forces' operating."
The phrase 'dark forces' is sometimes used about the state security services.
It was made famous by former royal butler Paul Burrell, who falsely claimed the Queen said it to him after Princess Diana's death in 1997.
Labour and the Tories accused Mr MacAskill of paranoia.
Despite releasing Abdelbaset al-Megrahi from jail in 2009, Mr MacAskill claimed Mr Salmond's trial had a higher profile than the prosecution of the Lockerbie bomber.
He said: "The Alex Salmond case was entirely unprecedented.
"For sure there have been major Scottish criminal trials from Oscar Slater through Lockerbie to numerous recent ones.
"But despite the notoriety of many and the horror of their crimes, none had the profile of Alex Salmond."
Mr MacAskill then compared Mr Salmond to Charles Stewart Parnell, the great Irish nationalist leader felled by an adultery scandal in 1890.
Not since Parnell "had there been the chance to bring down a major figure in an independence movement and no doubt with it to damage the cause", he said.
Mr MacAskill continued: "The fall-out from it is going to reverberate for some time within the SNP and - as a result - in both the independence movement and Scottish politics as a whole."
Mr Salmond was acquitted of 13 charges of sexual assault - with one found not proven - and later suggested he was the victim of a politically motivated plot.
He is now writing a book about the case to reveal evidence which was disallowed in court for legal reasons.
One of his supporters, his former SNP deputy leader Jim Sillars, has said the book will be like a "volcanic eruption" for the SNP, and the "rot" in the party may be so bad that the independence movement may need to set up a new party in its place.
Mr MacAskill said the actions of the Crown and Police Scotland "seemed to offer assistance to one side only rather than acting in the public interest for all".
He said much of the case against Mr Salmond seemed to be "offered up to Police Scotland on a platter by senior government and SNP sources; a prelude for the head they ultimately wanted to see placed upon it.
"The country was scoured from top to bottom, hundreds were interviewed.
"His entire adult life of over 40 years seemed trawled over.
"As a former justice secretary, I've known major police enquiries but never of such magnitude other than for the most heinous of crimes and dangerous of offenders.
"Despite all that, what they turned up was pretty flimsy.
"Some charges were utter bunkum and the likes of which I've never seen in 40 years involvement in the courts; and certainly not in the High Court."
Labour MP Ian Murray said: "Those who believe in 'dark forces' are usually found in the murky depths of social media promoting conspiracy theories, not the green benches of the Commons.
"Kenny MacAskill is a former Justice Secretary and sitting MP and should remember that was elected to champion the people of East Lothian, not his former party leader."
Tory MSP Annie Wells said: "The paranoid reference to 'dark forces' is hardly befitting of a former Justice Secretary and sitting MP."
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