The update to the Ministerial Code follows opposition complaints that ministers were trying to “block scrutiny” in the Scottish Parliament.
It had emerged some SNP MSPs appointed as parliamentary liaison officers (PLOs) also sit on the committee covering the same policy area as the minister for whom they work.
For example, SNP backbencher Jenny Gilruth is Education Secretary John Swinney’s PLO but she also sits on the Education Committee.
First Minister Nicola Sturgeon said the code would be updated to ensure PLOs will no longer be able to serve on the principal committee which scrutinises the portfolio to which they are attached.
She said: “MSPs who serve as aides to ministers do a vital job in terms of the required liaison between Parliament and Government.
“As such, it is important that they are able to carry out that function with the full confidence of both ministers and the parliamentary committees on which they serve.
“I believe that the parliamentary liaison officers who are currently in post fulfil that requirement admirably and there has been no evidence of any conflict of interest.
“At the same time, I have listened carefully to the case made by those calling for change, and so the updated guidelines I am publishing today will remove even the perception of any conflict of interest in the role of PLOs.
“The change is part of the updated Ministerial Code, which sets the highest standards of propriety and transparency for Scottish Government ministers.
“I will continue to lead by example in following the letter and spirit of this code, and I expect that all ministers will do likewise.”
Scottish Liberal Democrat business manager Mike Rumbles said: “The idea that a parliamentary liaison officer should help brief their minister for a committee hearing before crossing the floor and asking questions of them is patently ludicrous.
“The fact that the SNP had to be shamed into taking this basic step to preserve the independence of the committee system speaks volumes about their attitude to transparency and accountability.”