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Rather than opting for a percentage increase for all staff, the polytechnic and the Tertiary Education Union agreed to a $1100 flat increase.
TEU academic vice-president Phil Edwards said the vast majority of staff supported the agreement.
It was good way for the union and staff to address the significant pay gap between the lowest and highest paid workers at the institution, Mr Edwards said.
''It's just the right thing to do,'' he said.
''Most academics are probably pretty comfortable in terms of the amount of money they earn and what their total package looks like.
''And every now and then to put a lump sum on the rate means that they can acknowledge their lower paid co-workers.''
Otago Polytechnic was not the only institution that had agreed to a flat increase and it was becoming increasingly common across the tertiary sector.
The latest two-year agreement was the second time it had agreed to a flat increase.
The two agreements had made quite a difference to lower paid workers and equated to a roughly 4% increase for those earning $50,000 or less.
Last year, the University of Otago also agreed to a flat increase.
Its staff agreed to two pay rises of $850 and $1000 over two years.
At the time TEU organiser Shaun Scott said it was a good agreement for people who earned the least.
''They face the same increases in their cost of living, food for their families, pharmacy bills and school camps,'' Mr Scott said.