The Ministry of Education is warning there could be problems with the next two school pay days.
Errors in the Novopay system introduced in August have resulted in thousands of staff being paid incorrectly.
The ministry says the number of mistakes is declining but the pay days on 23 January and 6 February could go against the trend.
Those days will start or re-start the pay of about 40,000 staff who have moved schools or who are not paid during the holidays, and the ministry says some might miss out.
The Principals Federation says its members have reported problems getting their start of year details into the Novopay system, which does not bode well for the rest of the year
The ministry is confident the payroll system will get better.