Teachers and principals say a Qualifications Authority's watchlist shows small schools are having the most trouble with the National Certificate of Educational Achievement (NCEA).
The authority says the schools mostly have shortcomings in their systems and paper-trails for such things as guaranteeing students' work is their own.
The authority has seven schools on one-year audit cycles and all of them have small secondary rolls.
The Secondary Principals Association says teachers in small schools often find it difficult to check their NCEA marking is correct.
It says the schools might need more help paying for teachers to visit other schools.
The Post Primary Teachers Association says teachers in small schools need better access to professional learning and development that helps them get the NCEA right.
