Only two thirds of schools met the deadline to enter their end-of-year pay instructions into the Novopay system on Wednesday.
Schools were ordered to put data into the system by 5pm on Wednesday in order for staff to be paid correctly over summer.
Since Novopay was introduced in August hundreds of school staff have been underpaid or not paid at all.
But Ministry of Education manager Rebecca Elvy says the deadline is not fixed and expects reports to come in over the next few days.
She says the mInistry will individually contact each school that hasn't entered the information to offer assistance.
Ms Elvy says she understands the frustrations but the ministry assures schools it will help them get their reports in.
The Principals Federation says its latest survey shows that 90% of principals using the Novopay payroll system say they are still dealing with a huge backlog of problems from past pay rounds.
President Paul Drummond told Morning Report the Novopay system is not allowing many schools to complete and submit the information they need to put in.
He said he has no confidence that the system will be working properly by the end of the year.
The Australian company behind the new school payroll system has broken its silence about the problems, and apologised for the inconvenience caused by introduction of the $30 million Novopay system three months ago.
Principals' Federation president Paul Drummond says the apology is important and he is pleased Talent2 has acknowledged the stress its payroll system has caused schools.
Talent2 says the problems have come from a mix of human errors in its pay centres, technical problems and change-related difficulties for the school staff who use the system.