Annual fees for a Bachelor of Arts at the University of Auckland are about $6460.
Assuming the maximum allowable increase, moving from 4 to 3 per cent would save a student about $64.
NZUSA president Rory McCourt said that, given other rising expenses such as rents, this was a paltry amount.
"Fees will increase fractionally more slowly, but more students will clock up bigger debts, getting educations from institutions with less money to spend on quality."
The University of Auckland vice-chancellor Stuart McCutcheon has argued underfunding from the Government means institutions have no choice but to put fees up the maximum allowable amount.
However, Mr Joyce said Government funding to the university sector had grown by 20 per cent in the last six years, despite tough financial times in that period.
"When inflation is running at 0.1 per cent and is expected to be 1.8 per cent in the next year, allowing fees to go up by no more than 3 per cent is fair.
"It's important we strike a balance between maintaining the quality of tertiary education and affordability for students."
As part of the Government's child hardship Budget initiative, the student allowance rate for tertiary students with children will increase by $25 a week. This is expected to benefit about 9000 families.
Fewer people wanting to go to university or other tertiary institutions - driven by a decline in the population aged 18-25 and a stronger economy - has freed up money that will be invested in other areas.
Mr Joyce said much of that funding would continue the Government's push to get more people studying the "stem" subjects - science, technology, engineering and mathematics.
More than $97 million over four years will be given to institutions to increase their intakes in science, agriculture, optometry, pharmacy and physiotherapy. Total spending on the tertiary sector will increase by 1.4 per cent in 2015/16 to $3.06 billion.
The students
Isobel Gledhill is happy her university fees won't rise as steeply next year, but says the 60 odd dollars difference isn't enough to get excited about.
"It is not amazing, but it is definitely an improvement. I'm sure all of us at our flat will be relatively happy about that," Ms Gledhill said.
"At least [the fee increase limit] is not getting worse."
The 20-year-old lives in a flat in Mt Eden with other University of Auckland students studying commerce, engineering, arts and law.
The group, Ms Gledhill, Alex Yuen, Kate Kleinsman, Lauren Andrews, Laurie Ruddersmith and Justus Katzur, had hoped for other measures such as student allowances for postgraduate study.