David Caldwell, the new director of the Committee of Scottish Higher Education Principals, has denied that the committee is a "creature of the Committee of Vice-Chancellors and Principals".
He has warned that Coshep is prepared to oppose any CVCP line it feels is not in Scotland's interests.
A delegate at an Edinburgh University colloquium on Scottish higher education accused Coshep of having "scarpered indecently and unpatriotically back into the arms of the CVCP", in defiance of Scottish society's adoption of devolution.
Coshep now forms the Scottish arm of the recently revamped CVCP. But Mr Caldwell told the conference: "It has sovereignty in terms of policy formulation and where it comes to a different view from the CVCP view, it will not hesitate to articulate that."
The THES revealed last autumn that the two bodies had clashed over their submissions to the Cubie committee, although both subsequently minimised the row. Mr Caldwell said the relationship between the two organisations was "cooperative and helpful". Policy on tuition fees had been formulated in Scotland, but had won "valuable" CVCP support, he said.
Speaker Duncan Rice, principal of Aberdeen University, condemned the Scottish universities for having slipped into "uncritical acceptance" of the view that the dominant criteria for success were contributing to economic development, "relevant" degree programmes, short-term graduate employment goals, and impact on social mobility.
"We must fight to reassert our roles as educators for citizenship and leadership, and we must reaffirm aggressively our commitment to being reservoirs not just of humanistic knowledge but of wisdom and value," he said.
Lindsay Paterson, professor of educational policy at Edinburgh University, predicted that Scottish universities would become subject to the same level of "state intrusion" as schools and colleges. This would include not only scrutiny from the Scottish Higher Education Funding Council, the Quality Assurance Agency and the research assessment exercise.
"It will include directly political scrutiny from the committees of the parliament, assessing the cultural and economic contribution that higher education makes to the life of the nation, or to the nation's global competitiveness, or to the nation's fulfilment of its collective ideals," said Professor Paterson.