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Ministry of Social Development figures show more than 320 students in New Zealand, 50 of them from Otago, are making the most of an exemption due to be axed next year.
Some students on long programmes are able to claim allowances beyond the 200-week cut-off point, but the 2012 Budget has dispensed with that provision.
The New Zealand Medical Students' Association (NZMSU), and the Labour spokesman for tertiary education, Grant Robertson, have criticised the impending changes as having a disproportionate effect in relation to the amount saved.
Only a relatively small number of students will be receiving the exemption.
At present, students who are enrolled in a "recognised long programme", including medicine and law, are eligible for an extension to the 200-week limit on student allowances. Those retraining to be a teacher or for employment in an area recognised as being in the "national interest" are also eligible for the exemption to the 200-week cut-off.
This will change as of January next year when changes to student support announced by the Government as part of the Budget go through.
Figures released under the Official Information Act by the ministry showed 329 students received the allowance under the exemption as of April, about 90% of whom studied at universities. Fifty of those who received the allowance after the cut-off studied in the Otago region.
The figures also showed 70 University of Otago students received the allowance after the cut-off, suggesting a substantial number of medical students studying at Christchurch and Wellington campuses had successfully applied for exemption.
Otago University had the second most students out of any university receiving the allowance after the cut-off, behind the University of Auckland with 78 students.
Mr Robertson said the change would hit people from low-income backgrounds hardest and the "amount of money saved" thought the change was "disproportionate to the effect that this will have on individuals".
"I do think one of the impacts will be that some people from low-income backgrounds may avoid longer courses like medicine or veterinary science ... [which are] the kind of things we want people from all different backgrounds to study."
NZMSU president Michael Chen-Xu, who studies medicine at Otago University's Wellington campus, said many medical students, especially those from poorer backgrounds, relied on receiving the student allowance beyond the 200-week limit.
"It basically means that they don't have to worry about their finances when they study and can focus on the business of studying medicine," Mr Chen-Xu said.
The change could put some people off studying medicine and force others into part-time work, adding to what was already an "intense" workload.
A spokesman for Minister for Tertiary Education Steven Joyce said the Government made the change after deciding it was "important to focus student allowances on the initial years of study".
"It's important to note that a masters graduate on average earns up to 70% more than someone who doesn't go to university, and those with PhDs earn around 100% more," he said.