The Department of Education has confirmed ASTI members will receive a payment due for supervision and substitution duties in January if they reject the Haddington Road Agreement in the current re-ballot.
However, in a letter to the trade union, the department said in the event of a 'No', the department would then move to discontinue payments.
Members of the Teacher's Union of Ireland, who signed up to the deal, are not being paid for carrying out the same supervision and substitution work.
In a letter to the ASTI, however the department says the financial cost of not signing up to the agreement greatly outweighs the value of any payments due.
ASTI members are due to vote again in coming weeks on whether or not to accept the Haddington Road Agreement.
The Union's Central Executive Committee has recommended that they reject the deal for a second time. Ballots are due to be returned by 18 December.
Earlier, Minister for Education Ruairi Quinn said there is no question of ASTI members who vote against the Haddington Road Agreement for a second time being paid supervision and substitution allowances due in January.
Mr Quinn said it had been made "absolutely clear" to ASTI representatives that their members would not receive the allowances if they reject the agreement again.
The ASTI is the only public service union to reject the agreement.
Mr Quinn told the Dáil on Tuesday that the continued payment of ASTI members for supervision and substitution duties is unsustainable and cannot be continued.
Separately, the minister said he was "absolutely confident" that there would be adequate resources to implement proposed changes to the Junior Cycle from next September.
Mr Quinn acknowledged that the teachers have legitimate concerns that the system would not be ready and he said the department is prepared to discuss these.