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However, SIT chief executive Penny Simmonds said she was still worried about the future of the polytech after that period, and would continue to push to get the best outcome possible for the region.
"It was a constructive meeting. We raised our concerns - some points were clarified and some others not because they don't know the answers."
Mr Hipkins announced last month the merger of 16 New Zealand polytechnics into one tertiary institution.
The plan raised big concerns in the Southland region and a meeting was organised by Invercargill Labour list MP Liz Craig to discuss the vocational education reform.
SIT council deputy chairman Tim Ward, kaumatua Michael Skerrett and other southern mayors also attended the meeting.
Among her concerns were the composition of the subsidiary board, the international students recruiting process, the relationship between various boards and groups, the definitions of the regions and the online SIT2LRN distance learning programme, Ms Simmonds said.
The possibility of an ongoing parent-subsidiary arrangement was discussed during the meeting.
"We are reasonably comfortable with SIT autonomy for the next two years, but after that they don't know much. We will need to wait and see."
She would now wait for the draft of the reform Bill before commenting further.
After the meeting, Mr Hipkins said they had "a really positive discussion about the future of SIT" - while Dr Craig said the meeting was the first of many opportunities to discuss the matter.