The Post Primary Teachers Association has filed a class action against Acting Secretary for Education Peter Hughes over the Novopay fiasco.
The union signalled in February that it would take legal action on behalf of many of its 18,000 members who had been unpaid or underpaid as a result of the flawed payroll system.
The action, filed in the High Court at Wellington today, is against Mr Hughes because the union argues he has failed in his statutory duty to pay teachers.
The PPTA will be represented by Michael Reed QC and Paul Morten, who represented David Bain and recently won a damages case for Sir Bob Jones.
President Angela Roberts said it was a union's core business to fight for members' pay.
"Security of pay for people who work in schools is seen as so important it is protected by three laws the Wages Protection Act and the Education Act and the Employment Relations Act.''
She said the main relief sought was a statutory declaration, but sources said a claim for monetary remedies would be part of the case.
A Ministry of Education spokeswoman said the ministry respected the right of the PPTA to take such action but would be "defending it vigorously''.
"Our focus remains on fixing the issues with Novopay and we are making steady progress.
"The fortnightly pay runs have been stabilised, defects in the system are being resolved and the backlog clearance unit is making headway.''
The High Court proceedings are in addition to the individual cases taken on behalf of PPTA members.
The union said it had resolved 100 pay grievances for members before the cases reached the Employment Relations Authority.
Four cases had gone to the authority. Two had been settled successfully but details ave not been released.
Last week Minister Responsible for Novopay Steven Joyce released the findings of a Ministerial Inquiry, which found Cabinet Ministers had been misled by advice about the system from officials.
Ministry Deputy Secretary Anne Jackson resigned yesterday and another staff member was being investigated.
Last year former Secretary for Education Lesley Longstone resigned after a stormy relationship with Education Minister Hekia Parata.