Lord McCluskey, 70, Scotland's longest-serving judge, said the whole system should be reassessed to avoid the suspicion of "political cronyism".
His remarks follow a number of cases challenging the right of the Lord Advocate, Lord Hardie, a member of the Scottish Cabinet, to make judicial appointments.
These cases have all been appeals based on the European Convention on Human Rights, which was enshrined in Scots law in May this year. The convention gives everybody the right to be heard by a fair tribunal where the judge cannot be accused of impartiality because of his or her relationship with the Government.
Lord McCluskey, who is about to retire, said: "We may have to change the role of the Lord Advocate because he has ceased to be a wholly independent person by becoming a member of the [Scottish] Executive."
His comments, reported in a newspaper interview, are bound to cause alarm in England, where the Human Rights Act does not come into force until October next year. The dual role of the Lord Chancellor, Lord Irvine of Lairg, as head of the judiciary and cabinet minister, has been strongly criticised by legal reformers.
Last month the legal basis for the appointment of hundreds of judges was thrown into doubt when the Scottish appeal court ruled that the selection of temporary sheriffs breached the convention. This was because the sheriffs were appointed by the Lord Advocate, Lord Hardie, who is also Scotland's chief prosecutor.Reuse content