UCU Scotland, which represents lecturers, said the way the code was being drawn up ignored the views of staff and students.
The union is also concerned key recommendations of an earlier review – such as the election of chairs of universities’ ruling Courts – could be overturned.
Last year, a review of university governance recommended a new code of conduct to regulate the way institutions are run after warnings over the dictatorial style of principals and senior managers.
Michael Russell, the Education Secretary, entrusted the development of the code to the Committee of Scottish Chairs, which represents chairs of university courts.
Now, UCU Scotland argues they are ignoring a direction from Mr Russell to include representatives of staff and students on their steering group.
Gordon Watson, president of UCU Scotland, said: “In June, the Cabinet Secretary asked the chairs of court to lead a group, including staff and students, to develop a code of practice to take forward the report’s recommendations and we agreed. However, the chairs of court took over four months to develop a remit and form a steering group and, in blatant disregard of the Scottish Parliament, did not consult with staff or students.”
Mr Watson said the group proposed to “waste time, money and resources” re-gathering evidence that had already been considered by the earlier review.
He added: “Staff and student involvement in this process is vital if we are to make any meaningful changes to university governance to increase democracy and transparency.”
Dr Peter West, a former chair of court and a consultant in the development of the code, dismissed the concerns, saying: “We have already met with a number of trade unions including the UCU, and we will visit all universities in Scotland including separate meetings with staff and students.”