Patients should not be used as pawns in a pay row among doctors, according Minister for Health Simon Harris.
Many freelance doctors have refused to attend for work in emergency departments after their pay rate was reduced by €6 an hour.
There are concerns that a number of emergency departments may have to close because of the lack of agency staff; however all remain open at the moment.
Minister Harris said that the dispute needs to be dealt with through proper channels, and not by a wildcat strike.
"It's absolutely vital that our patients do not become pawns in relation to a dispute over pay," he said.
"Doctors' and nurses' pay in this country is actually rising, so this is not a pay dispute in terms of how much we pay doctors and nurses, this is about how much an agency is paid, and the fees of that agency then pays.
"It is important though that we encourage people to work directly for the health service, because as we know, we are too reliant on locum cover in this country."