Academics at Manchester University and the University of Manchester Institute of Science and Technology are demanding radical changes to charters and statutes designed to govern the proposed merged superuniversity to prevent a "centralisation" of power away from faculties.
The Association of University Teachers pledged to withdraw support for the merger unless changes were agreed before next month's deadline.
At an emergency AUT meeting, members passed resolutions signalling their alarm at the latest version of the charters, branding them a threat to academic freedom.
Paul Cammack, a Manchester professor and member of the university court, said the changes "reflect the outdated extreme top-down managerialism; they fail to match the vision of a great civic university of the 21st century".
Umist and Manchester said discussions with staff were ongoing. Alan Williams, of Manchester AUT, said a meeting on Tuesday with senior management had achieved "minor movement".