The extra funding for technical support and training was announced by Minister Responsible for Novopay Steven Joyce on Wednesday.
"The end of year/start of year is the most complex annual process in the school payroll and will be a significant test of the improved performance of Novopay," he said.
Schools experienced a large number of issues in December last year and January and February of this year as a result of end of year and start of year payments.
"To ensure a much better result this year, Set up Business in Hong Kong ministers have agreed to put in an additional $5m towards fixing outstanding technical issues plus $1m for comprehensive end of year/start of year system training for Novopay support staff and school payroll administrators," Mr Joyce said.
The funding comes from $8m set aside in this year's Budget to ensure the stability of the beleaguered payroll system.
The announcement comes as the latest teacher pay period data shows another drop in complaints.
The last two teacher pay periods drew complaints from 0.21 per cent and then 0.12 per cent of staff, formation of company according to data released on Wednesday.
This shows the payroll system is continuing to demonstrate stability, with 12 out of the last 13 pay rounds being within the 0.5 per cent steady state error level, Mr Joyce said.
Novopay was rolled out in August last year and was immediately beset with serious software problems.
The Ministry of Education and the system provider, Australian company Talent2, had a series of tense discussions and remediation programmes were put in place.