But Auckland vice-chancellor Stuart McCutcheon told the Herald that the increases were paid as a bulk fund and the university did not have to put it all into engineering and science.
"If we followed that, we would have increased the budgets of those faculties and made large numbers of people in the arts, creative arts, the business school and the law school redundant," he said.
Mr Unasa said the reality was that few Pacific students were studying engineering or science.
"The reality is that the students are studying the arts and particularly education, and enjoy and value and actually have a lot of success in those areas," he said. "For those Pacific students entering the university, who are not as many as there should be, even one or two of them [being shut out] makes a huge difference."
He said any cuts to those areas could threaten the university's Centre for Pacific Studies, which was "a central part of the identity of the Pacific community in Auckland".
"It has that community capital value that can't be measured in the jobs in science, engineering or medical sciences."
Another Pacific leader at the university, Dr Airini, head of the School of Critical Studies in Education, said more Pacific students needed to be recruited into engineering and science. "Mr Joyce is right. We do need to see that profile of Pasifika people in engineering. We also need to see that profile in education. It's not an either/or, it's a both/and," she said.
"This is actually about New Zealand's workforce development. We need to see a Pasifika presence in all of these areas because Pasifika are actually a big part of our younger population that will be essential for driving ahead NZ Inc's future."
Mr Joyce said the extra funding aimed to lift the number of engineering graduates with degrees or higher qualifications by 500 a year by 2017, but that did not have to mean cuts elsewhere.
Professor McCutcheon was not available for comment yesterday but issued a statement saying the university had been funded for an extra 150 engineering places next year.
He said the university taught 200 more engineering students than it was funded for this year and would be about 250 students above the funded places next year.
Skills standoff
Government:
Put $42 million extra into engineering schools to meet expected skill shortages.
Auckland University:
Funded for extra 150 engineering students next year, but wants to use some of the extra funding for other faculties.