The Auditor General has found most kura kaupapa Maori are free of financial problems.
It's been making checks on Maori immersion schools, after the Education Review Office in 2002 found many kura needed to improve aspects of their practices.
The audit has discovered 90% of kura have adequate budgetary controls in place.
But it notes 41% of schools recorded a deficit for the 2010, 2011 period.
Officials also report 18% of schools loan money to staff - a practice the Auditor General says is undesirable.
It warns that if advances are not repaid, they could lead to losses for the school and add unnecessary complications to the relationship with the employee.
The report says 13% of kura lack policies to fully address gifts, travel, credit cards, and entertainment.