The University of Auckland Council has voted to put up domestic student fees by 4% next year.
International student fees will also rise, by 5% in 2013.
Protesters occupied the university clock tower on Monday night in an attempt to stop the council voting for a fee rise.
Vice-Chancellor Stuart McCutcheon says the university faces a shortfall of funding each year and it either has to increase fees or reduce its services and staff.
But Student Association president Joe McCrory says the rising cost of a tertiary education is driving the country's best graduates overseas.