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One speaker at the public meeting of about 500 people made it clear how angry she was at the proposals.
"If I had sandals or something I would be giving it to you because you are flip-flopping all over the place.''
In his address Mr Hipkins paid tribute to SIT's achievements and said the Government wanted this replicated on a national scale.
He repeatedly stressed that no decisions had been taken and described the the proposal as "a framework'' in which to improve vocational training.
He said fears that SIT would lose its distance learning facility were unfounded.
His attempts to appease those in the audience appeared to fall on deaf ears and one speaker accused him of punishing SIT for being successful.
Invercargill councillor Toni Biddle said his decision would be detrimental to the community, the iwi, housing and future generations.
"I feel frustrated because there is a lot of smoke and mirrors and no guarantees. You never worried about Southland before, so why worry about us now? You don't want to be the minister that completely demolished the work that we have done for the last five years.''
He drew a rebuke from SIT CEO Penny Simmonds when he said that much was already decided nationally, including the institution's budgets.
Ms Simmonds pointed out that a third of SIT's did not come from government, but from other sources.
Speaking afterwards, she said much of what Mr Hipkins was saying was not in the proposals.
"We don't know how this works. We are lost about what he is saying here and what is written.''
Earlier, on arriving in Invercargill, Mr Hipkins was welcomed at Invercargill airport with a haka and a protest against his merger plans, which envisage merging 16 institutions into a New Zealand Institute of Technology.
Invercargill Mayor Tim Shadbolt, speaking in the afternoon, after Mr Hipkins held a meeting with the SIT Council, said Mr Hipkins had offered "nothing specific'' in terms of SIT's future.
"It was a lot of vague promises taking us into the promised land.''
He believed that Mr Hipkins had a good understanding of how people in Southland felt about SIT and the proposed plans to merge all the country's 16 institutes of technology and polytechnics into one mega New Zealand Institute of Technology.
Mr Shadbolt pointed out that SIT had been integral in turning around the fortunes of Invercargill.
But speaking before a visit to Waihopai Primary School, Mr Hipkins said that the community's understandably "passionate'' welcome had been fully expected.
He said that that while the country was moving to a national system it had to still be decided what would be run nationally and what would be run locally.