Lord Hamilton, the Lord President, has told MSPs the Public Services Reform Bill is “incompatible with the constitutional position” of the Scottish Court Service and causes him “concern”.

Dr Jim Dyer, the former Scottish parliament standards watchdog, has also accused the government of ­“political machismo” on the issue, the Sunday Herald can reveal.

The criticisms are the latest blow to the bill, fast becoming one of the most controversial of the current parliament. As the Sunday Herald reported last week, the proposed legislation would allow ministers to change, merge or abolish more than 100 public bodies.

Many agencies covered by the bill are currently independent of government, and were never meant to be under ministerial control. These include the commissioners for young people and children, freedom of information, and human rights.

Last week, in evidence to Holyrood’s finance committee, the bill was criticised as heavy-handed by the Law Society of Scotland, as well as by the independent commissioners.

In further written evidence to the committee, Lord Hamilton says the bill could see ministers use a parliamentary order to axe, without its consent, the entire Scottish Court Service (SCS), which underpins the judiciary “as a third arm of government”. Given the SCS was created by a full act of parliament, “it should ... not be capable of being abolished by the power which is sought to be created by this bill”. He goes on: “I would regard it as incompatible with the constitutional position of the SCS that any modification or transfer [of powers] could occur without the consent of the SCS.”

Dr Dyer said ministers seemed hell-bent on culling public bodies. “There are dangers in an approach which is too doctrinaire and which involves some degree of political machismo, eg deciding … that the number of public bodies and the number of scrutiny bodies should be reduced by an arbitrary figure of 25%, then working out the rationale for abolishing and merging bodies afterwards.”

A Scottish government spokesman said: “There are no plans to make changes to the Scottish Court Service. We are making public services simpler, sharper and better co-ordinated.”