A report by the Auditor-General shows some school boards have used taxpayers' money on unauthorised investments and personal expenditure, including traffic fines and satellite TV subscriptions.
Audits in 2011 found 33 schools borrowed more than they were legally permitted, 16 made loans to staff, 10 had conflicts of interest and six invested school money without approval.
However the Office of the Auditor-General says most of the country's 2500 schools are financially sound.
About 200 schools have debt levels which could affect their ability to pay the bills, and 45 are in serious financial trouble.
Teachers' and principals' groups say some boards of trustees lack financial experience, but the biggest reason for schools' money problems is lack of funding.
Post-Primary Teachers Association president Robin Duff says funding has slipped behind inflation and schools in poor areas, which don't have community funds to draw on, are suffering the most.
Secondary Principals' Association president Patrick Walsh says the report shows some boards struggle with the complexities of running a school, but the biggest problem is lack of money.
"There's a number of schools that are well governed and well managed, and it's simply that the resource pie that they have been given ... is simply not big enough."