Some teachers and gardaí have been warned they will lose pay increments from Friday.
The warning comes ahead of the Lansdowne Road pay deal's formally taking effect from Friday.
The ASTI and two Garda associations have both refused to sign up to the deal which will see partial pay restoration.
Public Expenditure Minister Paschal Donohoe said the Government had a duty to be loyal to the unions who accepted the deal.
He said: "We have to follow the law in this area, and it lays out a process in relation to what will happen if unions decide that they do not want to be part of the Lansdowne Road agreement.
"The benefits and protection of Lansdowne will be confined to the unions and members of unions that are inside the agreement."