Nicola Sturgeon has challenged Alex Salmond to prove there was a conspiracy against him, saying he has made claims "without a shred of evidence".
Mr Salmond is due to give evidence to the Holyrood inquiry into the government's mishandling of harassment complaints against him later this week.
He says he has "documentary evidence" of a "malicious and concerted" attempt to remove him from public life.
But the first minister said any claims of a conspiracy were "not true".
And she said Mr Salmond had an "obligation" to "replace the insinuation and assertion we have heard over several months now with evidence".
The Holyrood inquiry was established after the government conceded an internal investigation of two harassment complaints against the former first minister had been "unlawful".
He was awarded more than £500,000 in legal expenses following the judicial review case, and was subsequently acquitted of charges of sexual assault in a separate High Court trial.
In a written submission published on Monday, Mr Salmond said there had been "a deliberate, prolonged, malicious and concerted effort amongst a range of individuals within the Scottish government and the SNP to damage my reputation, even to the extent of having me imprisoned".
He said the government and SNP "felt threatened" by the judicial review case, and said he had "documentary evidence" that there was a "fishing expedition to recruit potential complainants".
In other letters to the inquiry he has described the behaviour of the government as a "disgrace", accusing it of concealing key evidence from his legal team and of leaking information to the media to damage him.
He has also accused Ms Sturgeon of "repeatedly" misleading parliament over her meetings with him, making statements which are "simply untrue", and of breaking the ministerial code.
Mr Salmond is to give evidence to the inquiry on Wednesday, with Ms Sturgeon expected to face MSPs the following week.
The first minister said she hoped Mr Salmond would "turn up to the committee and bring the claims he has been making out into the open".
She said: "He appears to be suggesting some kind of conspiracy or concerted campaign against him, without a shred of evidence.
"This is his opportunity - because the burden of proof of that lies on him, to replace the insinuation and assertion we have heard over several months now with evidence.
"I don't believe he can do that, because I know what he is claiming about a conspiracy is not true.
"If he can't substantiate it, it's time for him to stop making these claims - because it's not fair to women first and foremost who came forward with complaints, or the other people who have given years of loyal service to Alex Salmond who he appears to be directing those claims to."
In an interview with BBC Scotland, the first minister said she would "stand by what I said in parliament" about her meetings with Mr Salmond, saying she would "relish the opportunity" to go into detail.
She said: "I will set out what I knew and I will set out my recollection of all these things, and answer questions for as long as the committee wants to hear about that.
"This is a situation where I and others were faced with a really difficult scenario - allegations against someone I had been very close to. I dealt with that to the best of my ability and I think I made the right judgements overall."
Ms Sturgeon said the government "did make a mistake in the application of its procedure" for handling complaints, and said it would "reflect on the lessons of that".
But she insisted the new policy had been drawn up in response to "the global MeToo movement", not Mr Salmond.
This echoes evidence given to the committee by Permanent Secretary Leslie Evans - Scotland's top civil servant - who told MSPs that the government was not out to "get Alex Salmond".
Ms Sturgeon said she still had full confidence in Ms Evans, and that she expected her to remain in post for the duration of her current contract.