Some universities could run out of cash this year or breach their borrowing limits.
The Tertiary Education Commission made the warning in a financial overview of the sector delivered to incoming Tertiary Education Minister, Penny Simmonds in November.
It says it regarded Victoria and Massey universities as high-risk institutions and Lincoln and Waikato as medium-risk.
Those universities deny they will run out of money but they admit times are tough.
Education correspondent John Gerritsen spoke to Corin Dann.