Freelance doctors are "blackmailing" hospitals by holding a wildcat strike, according to a surgeon in one of the affected hospitals.
Some locum doctors have decided not to show up for work after the HSE reduced the hourly rate they are paid from €40 to €34.
Consultant Orthopedic Surgeon in Letterkenny Hospital, Peter O'Rourke, says a lack of contract staff gives the locum doctors extra power.
He said: "The hospital cannot recruit anybody else and they know that, so effectively they are blackmailing the hospitals into employing them or being stuck without anybody."
The Minister for Health Simon Harris has defended the cut saying the rate being paid to agency staff is still very competitive.
He said: "You have a situation where you could have a doctor who works for the HSE, who is similarly qualified doing the same work, working alongside a locum doctor and that locum doctor, even after the changes to the framework would be earning 36% more than them."
All emergency departments across the country remain open this afternoon, and it is unclear what impact any shortage of doctors may have.
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."