Teachers belonging to the Teachers' Union of Ireland will have to apply individually for payment of their next increment.
The payment is due under the Haddington Road Agreement, according to a Department of Education circular.
This is because the department has encountered data protection difficulties in differentiating TUI members from Association of Secondary Teachers Ireland members, who rejected the deal.
The two unions, which work alongside one another in 150 of the State's 729 schools, are now operating under different terms and conditions.
However, a problem arose in terms of how to differentiate TUI members, who are entitled to their next increment, from ASTI members, who are now subject to an immediate increment freeze.
Minister for Education Ruairi Quinn reiterated there was no way the Haddington Road Agreement could be reopened.
Mr Quinn was asked whether he shared the view of Minister for Expenditure and Reform Brendan Howlin that it would unsustainable for the ASTI to continue to receive supervision and substitution payments while the TUI did not.
Mr Quinn said it probably was unsustainable over time, but said he wanted to move forward and it was not an issue at the moment.
He said that any decision to cut supervision and substitution payments would be a collective Cabinet decision.
Mr Quinn said he would have to reflect on how to handle representations from non-union members who might want to sign up to Haddington Road, as it could set a wider precedent.
The TUI acknowledged that the department circular provided a mechanism for members to receive their entitlements under the agreement, including payment of their next increment.
TUI General Secretary John MacGabhann said the question of continuing supervision and substitution payments for ASTI members would be a matter for the Government and the ASTI.