University Entrance alone will not guarantee entry to half of the country's universities this year, and the Union of Students' Associations fears thousands of applicants will miss out.
Universities say it's too early to know how many might be turned away.
Four of the country's eight universities say students need NCEA level three, or level three with merit and excellence grades, to be guaranteed a place this year.
The benchmarks - higher than UE - allow the universities to manage enrolments if they look like exceeding the Government's enrolment caps.
Massey University vice-chancellor Steve Maharey says the new selection systems are likely to be permanent.
"I think we're creating a climate now where people understand they just don't enrol in university, universities are selecting them, increasingly, on the basis of their academic record - knowing that they are more likely to succeed because they do have a good academic record."
A fifth university, Waikato, also had a benchmark of NCEA level three, but has already decided it will not need to enforce it.
The Union of Students Associations says the change by the other four universities is a significant shift away from the cornerstone principle of open entry to university.
It says even more people from under-represented groups like Maori and Pacific people might miss out, and warns school qualifications are not always the perfect predictor of success at university.