Speaking to journalists on Friday, the Scottish Labour leader said “big issues” about the role of Parliament in holding the Scottish Government to account needed to be resolved.
Mr Sarwar said “huge questions” had been posed by the inquiry and founding principles of the Scottish Parliament have been “shaken” by the conduct of those involved in the Salmond inquiry.
The Holyrood inquiry into the Scottish Government’s handling of harassment complaints against the former first minister found significant failings by the government in both its complaints process development and handling.
The report was also critical of the Scottish Government’s approach to the successful judicial review action brought by Mr Salmond in 2018.
It also concluded First Minister Nicola Sturgeon had “misled” the committee on whether she had offered to intervene in the complaints process at a meeting with Mr Salmond at her house on April 2, 2018.
However a separate investigation, led by lawyer James Hamilton, found Ms Sturgeon had not breached the ministerial code based on her conduct during the process.
Mr Sarwar, who is attempting to move the debate on during the election from the “arguments of old” and away from talk of the constitution, outlined several aspects of Holyrood’s relationship with the Scottish Government that need to be reformed.
He said: “There have been huge question marks posed by the entire inquiry.
"There is the very principles of what our Parliament was created on, the principles of accountability and transparency I think have been shaken by that.
"I think we do need to look at fundamental reforms around our committee process. I think we need to look at reforms around how the will of Parliament is expressed and the actions governments are expected to take as a result of the will of Parliament being addressed.”
The Labour leader added: "I think we have to look at the civil service and the relationship they have with government.
"I think there are serious questions about the role of the Lord Advocate – I don’t mean as a personality, I mean as the position – and the separation of powers between the person that is the chief prosecutor in the country and the person that is also the chief legal adviser to the government.
"These are all big issues that I think we have to look at and resolve in the coming Parliament.”
Mr Sarwar insisted on Thursday that it was “not credible” that no-one had “taken responsibility” following the publication of the Holyrood report, which concluded the two women who made the allegations against the former first minister were “badly let down”.
He said: “I think there are still huge questions for the permanent secretary Leslie Evans. I think she has some serious thinking to do and should be considering her position.”
His comments came after Mr Salmond announced he plans to take legal action against Ms Evans.
In a statement on Wednesday, the former SNP leader insisted such a move was necessary to “prevent a damaging erosion of trust in the institutions of government”.