Thousands of workers have closed beds and cancelled operations over the past week in their fight for a pay increase of 15 per cent over three years.
They also plan to walk off the job for 24 hours from Monday.
The Director General of Health Kim Snowball says he has written to all nurses advising them they must comply with the orders.
He said the letter was necessary to outline the potential consequences of their work bans because the Federation was telling its members they will not face any disciplinary action.
"We want to work with nurses," he said.
"Nurses do a fantastic job in our state.
"This is not about an attack on nurses this is actually about supporting patient safety but also reminding the union and the nurses that the Commissioner has ordered them to stop that industrial action."
The Federation's Mark Olsen says the threat is outrageous.
"I'm disgusted that the Director General would threaten to discipline or deregister any of our members because of their activities with the industrial action," he said.
"Over the last 15 years nurses and midwives have closed beds in various industrial campaigns both in WA and other states.
"No nurse or midwife has ever been sacked, suspended or deregistered in the course of these activities."
Mr Snowball has confirmed he will sit down with Federation on Sunday afternoon.
"We're not about standing in the way of a good wage increase for nurses.
"We are simply saying these bans have got to stop.
"They are now harming patients safety and we need to act to respond to that."