The Ministry of Education says about 400 schools have not yet completed the end of year process that ensures their staff are paid during the school holidays.
Some schools have had trouble entering information into the new Novopay system and the ministry has been contacting all 2400 schools to help them.
It says the holiday pay details affect about 10,000 support staff, relief teachers and teachers who are changing jobs next year.
Schools were told to enter their end of year information by Wednesday last week. By Monday night, 85% had done that.
Meanwhile, the ministry says it will delay a review of its pay unit until the problems have been fixed.
The Public Service Association says the decision is a victory for common sense and provides breathing space for staff who have been working long hours on Novopay.
The association says the ministry had wanted to reduce the number of staff in the unit from 23 to 14.