Northern Territory teachers are set to be the highest paid in Australia under a new pay deal.

More than 90 per cent of teachers have voted in support of the new Territory government's pay offer of a 12.9 per cent pay increase over three years.

NT Minister for Education and Training Jo Hersey said the agreement would support Territory schools to "retain and attract teachers at a time of a national workforce shortage in education".

Other benefits include a $1000 increase in the Katherine and Alice Springs Attraction and Retention allowance, which is now worth $4500 per year.

More than 40 per cent of students in the Territory's school students are Indigenous.

Ms Hersey acknowledged the Australian Education Union executives, representatives of the Department of Education and Training, and the Office of the Commissioner for Public Employment "in crafting an agreement that recognises the work of teachers, principals and Aboriginal team teachers that work each and every day to improve the life of young Territorians".

"Over the life of the agreement, the increase represents a 13.46 per cent compounded pay rise," she said.

As part of the deal, the NT Department of Education and Training has committed to developing a "Hard To Fill School" incentive payment scheme to assist in attracting and retaining employees and help balance the workload in these schools

"The Territory must be competitive if we are going to attract and retain excellent teachers and this deal delivers the country's best pay deal," the Minister said.

The Commissioner for Public Employment will now lodge the agreement with the Fair Work Commission for approval.

"Now our governments focus for education is on the safety of teachers and students, and on getting kids to school," Ms Hersey said.

"To support teacher workloads and enable greater time to plan and prepare to deliver quality education to students, primary school teachers will receive an additional 1.5 hours per week to be phased into implementation from 2026 onwards."

The minister also said class sizes will be reduced from an average of 27 to 25 students in transition and Year 11 and 12 classes.

Until the new agreement is approved, and starts, the current Northern Territory Public Sector Non-Contract Principals, Teachers and Assistant Teachers' 2021-2024 Enterprise Agreement continues to apply.