Tertiary Education Commission figures show universities and polytechnics carried $33 million worth of unsubsidised students last year.
The students were not subsidised by the Government because they were above agreed enrolment levels.
But they paid fees and they were eligible for student loans and allowances.
Because of the cost of loans and allowances, tertiary institutions are discouraged from exceeding the value of their subsidised enrolments by more than three per cent.
The commission's figures show Waikato and Massey universities and Tairawhiti Polytechnic exceeded their subsidised enrolments by more than 6%.
Nelson-Marlborough Institute of Technology neared 6%, while the University of Canterbury and the Southern Institute of Technology were more than 4%.
Waikato and Massey say they will try to remain within 3%, but Lincoln and Otago universities warn they may exceed that figure.
