The Tertiary Education Union says job cuts will follow tougher rules to claw back money from institutions that enrol fewer students than the Government has funded them for.
This year universities, polytechnics, wananga and private tertiary institutions will have to repay money if they fall more than 1% short of their agreed enrolments, a lower benchmark than the 3% threshold in place last year.
The tertiary sector says achieving the exact number of student enrolments for which they have been funded is like landing a jumbo jet on a 10 cent piece.
The Tertiary Education Union says small, regional institutions will find it hardest to cope because small changes in student numbers will drop them below the 1% threshold.
Union president Lesley Francey said the change is a "cynical attempt by the Government to slash funding" without it being obvious to the public that that is what is is doing.
However Tertiary Education Minister Steven Joyce does not think educators will struggle to fall within the margin of error or that there will be any job cuts.
"It's just trying to get absolute value and wasting $35 million a year on funded provision which is not being used is a bit tough to get taxpayers to accept," he told Radio New Zealand's Morning Report programme.