The Otago Polytechnic branch of the Tertiary Education Union (TEU), representing more than 430 staff, described concerns about the amalgamation with Te Pukenga, which is uniting 16 institutes of technology and polytechnics nationally.
Te Pukenga recently concluded a three-week feedback period on its organisation and leadership structure proposal, designed to uphold its charter.
However, the TEU submission called for more information, saying many factors were still unclear as the formal transition date of October 31 drew nearer.
"Our members [need] clarity and detail to understand the direction of Te Pukenga and where they fit in this new organisation," the submission stated.
Lack of funding was a recurring issue.
"Without a funding system that supports the function of Te Pukenga outlined in the charter, our members feel that we are being set up to fail."
The annual forecast deficit of Te Pukenga was set at $110 million earlier this year, but an updated deficit forecast now sets the figure at $63 million, achieved in part by not replacing staff who leave.
Loss of knowledge and increased overall workloads for remaining staff were the result of this "austerity measure", the submission warned.
"This has an impact on staff morale."
Members were also worried the terms and conditions of their employment would change if Te Pukenga took a unified approach across its branches.
"It is mentioned often that Otago Polytechnic kaimahi [staff] enjoy some of the best terms and conditions over the Te Pukenga network, and there is no funding available to use this as best practice across the whole of Te Pukenga.
"This has created stress and uncertainty for members who are unsure what this will mean for their work conditions in the future."
The possibility of some courses being removed because of low numbers or not meeting financial targets was also "a huge concern".
Members were also being asked to sign employment variations on faith, without details of how the organisation would be structured, the extent of head office control and how this would affect staff, students and communities.
TEU members at Otago Polytechnic had engaged with the transition process for two years with little action from Te Pukenga, and some were questioning the confidence they should place in the organisation, the submission stated.
"Trust needs to be rebuilt and staff need to feel their feedback is being heard."
Otago Polytechnic chief executive Dr Megan Gibbons said the uncertainty of the transition was "unsettling" for staff.
"We are doing all we can to support staff through this and Te Pukenga has committed to providing certainty as soon they are able," Dr Gibbons said.
However, it was encouraging to see the level of engagement from staff, she said.
An announcement was due to be made late this month.
The transition would take time and pose challenges, but would also present opportunities to better serve students and employers.
"We are always looking at the demand for our programmes and listening to employer needs in our region."
Te Pukenga chairman Murray Strong said feedback on the organisation and leadership structure proposal numbered in the thousands and was now being analysed.
Decisions would be shared with staff and the public along with a summary of key themes and feedback, Mr Strong said.
"We are going through a major change process, and I acknowledge that has an impact on staff wellbeing."
The organisation would be structured to minimise impact, with detail to come in stages over the coming months and into the new year.