Universities have told a government advisory group they are making significant losses on courses that spread a small number of enrolments across several institutions.
Meanwhile, Business New Zealand has warned that universities should not conduct their own quality assurance, and the Tertiary Education Union has decried what it describes as the "financialisation" of universities.
The University Advisory Group has run two rounds of consultation on the future of universities, the most recent closing at the end of last month.
An interim report to the government - due last month - would now be provided at the end of September, with a final report due next year.
The review was headed by Sir Peter Gluckman, who was also chairing a separate but linked review into the science and research system. The reviews were set up to advise the government on how universities and science could increase productivity and economic growth.
The university review posed questions including whether there was a right percentage of foreign enrolments, the right size of the domestic student body, and what was the purpose of universities.
Universities New Zealand's submissions warned against changes that would force universities to specialise further and offer fewer courses in common.
It said the eight universities were only superficially similar and it was important to ensure students could access a variety of courses at their local university.
But it said polytechnics' degrees should be more greatly differentiated from those of universities.
The submission said the review group was considering a Higher Education Ministry or a Higher Education Council, but universities did not support those suggestions. Instead it recommended an advisory group that could work with government at a high level.
The submission listed subjects - including geophysics and oceanography - where several universities each had just a handful of students in Bachelors-level study.
"Assuming at least half the students enrolled in modern languages, performance (music, drama, etc), and classics are also in programmes where there are similarly low ratios of enrolments per institution, we can estimate that at least 1 percent and possibly as many as 2 percent of all students are in programmes that are significantly loss-making for the institution due to very low enrolment volumes. That is somewhere between 1500 and 3500 students," the submission said.
It said universities needed a funding system that would help them to share teaching of subjects with few enrolments.
Universities New Zealand chief executive Chris Whelan told RNZ the fundamental issue for the sector was inadequate funding.
"From our perspective there's a lot of interesting questions being asked but none of them are likely to lead to major settings changes. The sort of things they're looking at are you know, are there different ways of doing strategy or policy around the sector. Of course there are but every single one of is going to involve a different set of trade-offs to the ones that we already have."
Whelan said the government could relatively easily change the funding system so it was easier for universities to share courses that had relatively low enrolments, but were in the national interest.
The Tertiary Education Union's submissions said universities had lost sight of their purpose.
"Instead of operating in the interests of the public good, there has been an overt drive toward ensuring economic productivity above all else," it said.
Union national secretary Sandra Grey told RNZ the biggest problem for universities was under-funding.
"It's not the only thing that we hope is addressed through this review and the actions that will follow it, but it is fundamental. We can't keep going on the smell of an oily rag, we can't keep providing quality public tertiary education as a public good unless the sector's funded properly," she said.
She said the union wanted the advisory group to recommend changes that would treat the eight universities as a system rather than as competitors.
"At the moment we have eight competitive universities all competing in a very small country for the same students, the same research funding, the same input from industry. If we could treat it more like a system and do much more collaboration that would help some of the funding issues," she said.
The Association of Scientists' submission said universities' qualifications were increasingly mismatched to student needs.
It said universities needed more funding for low-demand subjects and there was too much competition between universities.
Business New Zealand told the advisory group universities could save a lot of money by extending their use of online lectures.
It also recommended more technology transfer from universities to business, and improved governance.
"We recognise, however, that the principles of academic freedom and institutional autonomy are greatly cherished by those who work in the universities. This means that change is likely to be uncomfortable. But we believe that, in the interest of all New Zealanders, the government should be determined in its pursuit of change in the system," it said.
Business NZ said universities should not be allowed to run their own course approval and audit processes.
"By having the universities run all aspects of quality assurance as a collective, external scrutiny is minimal, including channels for businesses to connect on industry developments that could be incorporated in teaching, learning and research," it said.
It said the Qualifications Authority was not the right agency to moderate degree approvals and content, and it recommended creating a new agency.