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Western Australia is probably the largest user of FIFO so it will feel the impacts the most.
Under the rules announced by WA premier Mark McGowan, unless exempted, arrivals from other states in Australia will be ordered to self-isolate for 14 days.
Exemptions apply to essential services and workers, including health and emergency services, defence and policing, mining industry workforces, flight crews and freight of essential goods, via ports and trucks.
Nevertheless, miners are bracing for some operational impact.
Chamber of Minerals and Energy WA chief executive Paul Everingham said all non-essential staff had been sent home and FIFO flights would be "massively curtailed".
"We're taking extraordinary measures to ensure our workforce and the communities in which we operate are not impacted," Everingham said.
It is understood about half the 5000 interstate workers have been sent home.
FIFO workers living internationally will have to self isolate if they are returning to work.
WA is not the only state bracing for FIFO impacts.
Queensland Resources Council chief executive Ian Macfarlane said the state's resources sector was working through what the new arrangements would mean.
"QRC and our industry continues to work with all levels of government," he said, pointing out that the national cabinet had declared mining an essential activity.
"In relation to FIFO operations, the Queensland resources sector is working with the state government to implement protocols to assist with the separation of the community and FIFO workers while in transit," Macfarlane said.
"This will ensure the resources sector can continue to deliver its much needed economic benefits to the economy by producing commodities and employing people."
Minerals Council of Australia CEO Tania Constable said the overriding priorities and concerns for the industry remained protecting the health, safety and livelihoods of workers, contractors and communities, continuing the movement of essential operational staff, including between states and maintaining flight, rail and port networks to supply fuel, equipment and other critical inputs.
"The sudden shift by different governments in recent days to place restrictions on movement of people across borders prompted the MCA to accelerate work on the national approach to the safe and efficient passage of essential workers and supplies for mining operations," she said.
"This work is continuing with the MCA joining other resources organisations in a united approach to the National Cabinet on these vital issues."
According to Fortescue Metals Group CEO Elizabeth Gaines, the company had factored this development into its scenario planning and had been working with the resources industry and the WA government to ensure its operations continue and it kept access to site critical operational roles.
