The Post Primary Teachers Association and the Educational Institute are unhappy teachers are losing their right to elect members to the body that registers and disciplines them.
The Government is next year replacing the Teachers Council with a new organisation, the Education Council.
In the process, early childhood, primary and secondary teachers and principals will lose the right to elect four of the council's members.
The teacher unions and School Trustees Association will also no longer nominate three of the members for the Government to appoint.
Instead, the Education Minister will appoint all the Education Council's nine members.
The two teachers' unions say the change contradicts the council's goal of leading and representing the teaching profession.
Post Primary Teachers Association president Angela Roberts says tthe decision is very disappointing and teachers will be fighting it hard through the select committee process.
