The lodgement comes as Nicola Sturgeon denied that a senior official from within the Scottish Government did pass on the name of a complainer to Mr Salmond’s former chief of staff.
A statement from the former first minister’s spokesperson said a complaint had been lodged under the civil service code.
The spokesperson said: “Mr Salmond has lodged a formal complaint with the Permanent Secretary to the Scottish Government under the civil service code, on the conduct of the official who is alleged to have breached civil service rules, by disclosing the name of a complainant in the Scottish Government process.”
During her evidence session at the Salmond inquiry, Ms Sturgeon confirmed that such a breach would be a sackable offence.
However, she said that “to the best of her knowledge” that had not taken place and questioned the accuracy of the claim from Mr Salmond despite corroboration from Kevin Pringle, the SNP’s former communications chief, and Duncan Hamilton, Mr Salmond’s legal adviser, described as “hearsay” by the First Minister.
Ms Sturgeon said these issues around complaints against Mr Salmond were “deeply personal”.
She said: “This stuff is deeply personal for me and it is really quite hard to talk about and at times if I have appeared as if I’m cagey about it, that is one of the reasons.
"I was really, really worried that anything I said about this at any time would cause headlines, news, commentary. I was always trying to avoid doing that, so if I appeared as if I was not being as open and discursive and full, that was another of the reasons.”
The First Minister said the allegations linked to a Sky News query had left her with “lingering suspicions” of potential complaints against Mr Salmond and was asked whether she understood claims she had misled people in answers to questions from media following the news of complaints against Mr Salmond breaking.
She said: “As far as I knew, there was nothing to it, although I did have some concerns that there might be something to it, so I had nothing to base that on beyond what I’m telling you here.
"Yes, I do understand why people might see that, but I would just say to people that there are a lot of factors here.
"I have seen commentary to the effect that I always seem really uncomfortable when I speak of this, I am really uncomfortable when I speak about this.
"We are talking here about serious allegations that have led to the breakdown in a relationship with someone who was really important to me on all sorts of levels, so I do feel really uncomfortable when I speak about this at a human level.”
The Salmond inquiry is examining the botched handling of harassment complaints against Mr Salmond by the Scottish Government, which led to a £500,000 legal bill after the Government conceded a judicial review challenge on grounds the process was “tainted by apparent bias”.
Mr Salmond was also acquitted of sexual offence charges in a trial last year.