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Prof Hayne said members of the education and science select committee did not pay adequate attention when listening to her and other people making submissions on the Education Amendment Bill, Radio New Zealand reported.
Universities and students' associations have labelled the Bill - which includes decreasing the size of university councils - as an attack on democracy and an attempt by the Government to gain increased control over universities.
Labour tertiary education spokesman and committee member Maryan Street told the Otago Daily Times Prof Hayne had every right to feel aggrieved as National MPs on the committee had lost interest after hearing concerns about the Bill from about 300 submitters.
''The Nats are switching off. Generally, there is only one or two of the National party MPs present who pay any attention at all,'' Ms Street said.
This prompted Ms Street to apologise to Prof Hayne for the way she had been treated by the committee - something she felt the chairman, National MP Cam Calder, should have done.
Prof Hayne made the comments when taking part in a second submission on behalf of Universities New Zealand on Wednesday, after submitting on behalf of Otago University a week earlier.
She told MPs on the committee they displayed a poor attitude when listening to her and students' associations submissions last week.
''As an academic who has spent more than 20 years in the classroom listening to and working with young people, I was very disheartened by the dismissive and cavalier way in which they were treated.''
Mr Calder disagreed with Prof Hayne's and Ms Street's comments, saying all submitters were treated with ''courtesy and respect''.
''We value the democratic process,'' he said.
Prof Hayne said yesterday said she did not want her ''opening comments to detract from the substance'' her submission.
The ''most important thing'' she had to say was about the proposed changes to the legislation. ''From time to time, we can all benefit from feedback on how we are perceived by others.
''I provided that feedback and the select committee responded positively to correct it.
''Now, we need to get back to the matter at hand, which is the change to legislation,'' she said.