Minister for Education Ruairi Quinn has warned ASTI secondary teachers they will lose their protection from compulsory redundancy after rejecting the Haddington Road Agreement.
The ASTI, which has threatened industrial action from next week, is the only public service union to reject the deal.
Speaking in the Dáil, Mr Quinn said the ASTI decision means the protections and benefits of the agreement, including those in relation to security of tenure of employment, are not available to its members.
He said this would be a matter of concern to many teachers, in particular young, newly-qualified teachers.
Mr Quinn said in addition to the monetary impact on individual teachers, the agreement also provides additional benefits for young teachers, particularly in relation to securing permanent status as teachers.
The minister said he was extremely disappointed the ASTI had rejected the agreement and he urged it to reflect carefully on its decision.
He said teaching was a valued and important profession in Ireland and said he was glad agreement had been reached with the three other teaching unions.
Secondary school pupils, parents, school managers and the Government have been coming to terms with the fact that serious industrial disruption could lie ahead in the State's secondary schools.
The ASTI said yesterday it would withdraw from all meetings that take place outside school hours in protest at cutbacks in pay and conditions.
The union has also decided to withdraw from in-service teaching for the Junior Certificate cycle.
No member will take on a vacant post of responsibility without being paid for it.
Earlier, the Teachers' Union of Ireland, which accepted the deal, instructed its 15,000 members not to take on work normally done by ASTI members.
ASTI members will be working under lesser terms and conditions than TUI teachers following the rejection of the agreement.
Members of both unions work side-by-side at around 120 out of 720 secondary schools.
In a statement on the TUI website, its President Gerard Craughwell and General Secretary John MacGabhann said the two unions are in close contact with a view to ensuring that their respective positions are acknowledged and respected.
They said that in accordance with normal trade union practice, no member of the TUI, including principals, deputy principals and other post holders, should undertake work normally done by ASTI colleagues.
The TUI said further advice will be issued following talks with its ASTI colleagues.
Members told to continue substitution duties
Meanwhile, the ASTI has instructed its members to continue to cooperate with supervision and substitution duties in school, as they are voluntary and attract payment.
Teaching unions that accepted the Haddington Road deal will no longer receive supervision and substitution payments totalling up to €1,700 a year and in future teachers will not be able to opt out of the duties.
Ironically, because the ASTI has rejected the Haddington Road deal, its members will continue to receive the payment, and will be entitled to refuse to carry out the duties.
A spokesperson for the Department of Education and Skills said the only way the payment could be cut would be if the minister decided to change their terms and conditions, which he now has the power to do.
She said that has not yet happened, but that all options were being considered.
Schools were forced to close during a dispute in 2002 when teachers refused to do supervision and substitution.
Earlier, the ASTI said the affect on students of forthcoming industrial action in schools will be "marginal".
Speaking on RTÉ's Morning Ireland, ASTI General Secretary Pat King said the dispute was not about money, and teachers are available to meet Government representatives to discuss their position.
He said: "We are complaining about changes in structures. It's not about money. It's not about pay and we're available."
Mr King said the union was not intending to affect students in any way, adding that the action was deliberately targeting administrative work.
Asked whether classes would be cancelled to facilitate rescheduled parent-teacher meetings, he said: "It will be a marginal effect on students.
"We are not taking strike action and our intention is to protect education as far as we can.
"Our dispute is about the quality and disintegration of education."
Earlier, Minister for Finance Michael Noonan said there was no room for renegotiation of the agreement.
Speaking on his way into a Cabinet meeting, Mr Noonan said his colleague Minister for Public Expenditure and Reform Brendan Howlin had handled negotiations very effectively.
Mr Howlin also appealed to the ASTI to reflect on its decision to reject the deal and said the agreement could not be changed.