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"I urge the minister and his officials to take heed of them.
"Mr Ker is the leader of one of New Zealand's most successful polytechnics. He is someone who is widely respected within the tertiary sector for his sound strategic judgement in relation to the [industry training providers] sector, and vocational education," Prof Hayne said.
Consultation on the proposal will close on March 27.
Mr Ker said he was "thrilled" at the university's response, but he did not want to speculate on whether the university support made it any more likely the head office for the new system would be in Dunedin, another idea he was keen to see implemented.
The Government's proposal was for a "New Zealand Institute of Skills & Technology" to manage capital and operational budgets, staffing, student and learning management systems for all polytechnics.
Mr Ker suggested aspects of administration - for instance a curriculum service and back-of-house services such as IT, finance, HR and payroll - could be shared between polytechnics.
He is keen for power over what to teach and how to assess, international student recruitment policies and detailed budgets remain with individual polytechnics.
The Otago Secondary Schools' Principals' Association has said it also supports the Otago Polytechnic. An association spokesman described Otago as "a successful and innovative organisation that is meeting student need in Otago and beyond.
Alongside the university and polytechnic, Te Wananga o Aotearoa has a campus in Dunedin.
Te Wananga chief executive Te Ururoa Flavell said the wananga was considering the implications of the reforms.
"It is working with the Minister of Education and officials on the detail for the wananga sector. Our priority is Maori educational achievement and we plan to continue working closely with the Government to ensure this remains a focus through these reforms."