It follows claims the former SNP leader was reported to police over his conduct towards two staff members at his official Bute House residence in 2013, according to the Daily Record.
In a lengthy statement on Twitter, Mr Salmond denied the claims and said he has been prevented from properly challenging them by Scottish government procedure.
He wrote: “For many months now, and on the advice of Senior Counsel, I have attempted to persuade the Permanent Secretary to the Scottish Government that she is behaving unlawfully in the application of a complaints procedure, introduced by her more than three years after I left office.
“This is a procedure so unjust that even now I have not been allowed to see and therefore to properly challenge the case against me. I have not been allowed to see the evidence.”
He added: “The Permanent Secretary chose to deny me contact with any current civil servant, many of whom wished to give evidence on my behalf, and access to documentation to allow me to properly challenge the complaints, all of which I refute and some of which were patently ridiculous.
“It is therefore with great reluctance that I have today launched a Judicial Review in the Court of Session which will decide the issue of the lawfulness of the procedure which has been used against me.”
A Scottish government spokeswoman said: “We can confirm that Alex Salmond has initiated legal proceedings against the Scottish Government and as a result we are restricted in what we can say.
“However, the Scottish Government will defend its position vigorously. As a matter of principle and integrity, it is vital that any allegations of harassment are treated seriously and investigated thoroughly, regardless of the identity of the party involved.”
Police Scotland have not commented on the Daily Record report.
Mr Salmond stepped down as first minister after losing the independence referendum in 2014 and was replaced by Nicola Sturgeon.
He lost his seat as MP for Gordon to the Scottish Conservatives in last year’s general election.