The Deputy First Minister stressed the Government was not planning to release information about the "substance" of the claims about the former first minister.
Instead, the Government will ask the courts for permission to release documents Mr Swinney says "relate directly to the committee's remit and to questions asked of us".
The Committee on the Scottish Government Handling of Harassment Complaints has been embroiled in a long-running dispute over the release of evidence.
In a letter to convener Linda Fabiani, Mr Swinney takes umbrage with the suggestion the Government would release documents with details of the allegations.
He said there has been "misrepresentations of some of the Scottish Government's actions contained in some of the submissions made to your committee".
Mr Swinney wrote: "The committee has made it clear it does not wish to receive such information - a position we have understood since the outset and agree with, not least because releasing that information would risk identification of the individuals who made complaints.
"I also want to be clear that the Scottish Government's legal action, to which you also refer, is not seeking the court's permission to submit to the committee information about the substance of the complaints."
Mr Swinney claimed the Scottish Government had "no choice" but to ask the Court of Session for permission to hand over certain documents to the committee because of an objection from an individual - believed to be Mr Salmond.
Mr Swinney, who is leading the Government's response after Nicola Sturgeon recused herself, said: "These documents are directly relevant to the questions asked by the committee, they remain in existence and in the possession of the Scottish Government, and we wish all the relevant information to be provided to the committee"
Lawyers acting for Mr Salmond said they were now gathering relevant documents they are legally able to provide.
In a letter to the committee, Mr Salmond's lawyer David McKie said: "We note that while such progress in relation to giving the committee sight of documents from the civil case is to be welcomed, our client remains under severe restriction, and indeed threat of prosecution, in relation to seeking to assist the committee by making reference to directly pertinent evidence which emerged as part of the criminal investigation. "
The correspondence follows confirmation from the Court of Session's principal clerk that it cannot provide all evidence sought by MSPs without a court order.
Ms Fabiani wrote to the court to request the release of all evidence relating to the case in an attempt to bypass legal wrangling and disagreements between Mr Salmond's lawyers and the Scottish Government.
In her letter to the court, the SNP MSP said the Scottish Government's "previous refusal to provide documentation" had delayed the committee's inquiry.
Pledging to comply with all legal restrictions, Ms Fabiani: "We consider that having sight of some of the court documents is essential to enable the committee to meet the terms of its remit."
In her reply, principal clerk Pam McFarlane said the court could provide copies of court orders and Judge Lord Pentland's notes of 4 October and 14 December 2018.