Half the country's public tertiary institutions enrolled fewer students than they were paid for last year but only five have to repay any money.
Tertiary Education Commission figures show the value of education delivered by the 29 universities, polytechnics and wananga was more than $27 million below the what was paid for by the Government.
The Canterbury earthquakes and a slump in enrolments in the second half of 2011 contributed to the under-delivery.
The shortfall left two universities and five polytechnics more than 3% short of what the Government paid them, which is the point at which repayments must be made.
However two of the institutions were exempted because they were hit by the Canterbury earthquakes.
Nine other institutions under-delivered but were within the 3% threshold and do not have to repay anything.