From 12:01am this morning, people in the Perth and Peel regions are only allowed to leave their homes for essential reasons until at least 12:01am Saturday.
In previous lockdowns, fly-in, fly-out workers had been deemed essential.
However, McGowan said last night he had asked the mining industry to limit travel within WA.
"The four-day lockdown announcement for Perth and Peel by the WA government will have an impact on FIFO movements," Chamber of Minerals and Energy of Western Australia CEO Paul Everingham said.
"WA government directions stipulate that only employees critical to ‘ongoing operations' will be allowed to travel outbound from Perth/Peel.
"This will likely result in slightly longer shift rosters for those currently on site."
The Association of Mining and Exploration Companies said in relation to FIFO, the definition of essential workers had been significantly narrowed to "mining for the purpose of critical maintenance and to avoid significant losses".
"This is described as a limitation on FIFO mobilisation from the affected (Perth and Peel) area," AMEC said.
"Although the definition is not entirely clear, it is understood that the intention from government is that the vast majority of the FIFO workforce should not be, and is restricted from, travelling."
AMEC noted the essential worker definition also included "building, maintenance and construction services".
"It is not clear whether this enables mining industry workers to travel for the purposes of project development. Further clarity is being requested," it said.
A look at the Perth Airport departures page this morning showed that while many FIFO flights had been cancelled, the majority went ahead as planned this morning.
Tanami mine cluster
The COVID-19 outbreak at Newmont Corporation's Tanami gold operations in the Northern Territory has grown to seven.
The NT recorded one new case yesterday, a male worker who was already in quarantine at the Howard Springs Quarantine Facility when his positive test was returned.
Five cases are in the NT under the care of NT Health at the Howard Springs Quarantine Facility and there is one case each in Queensland and New South Wales.
McGowan described the outbreak this morning as a "frightening event" but so far, all 177 Tanami workers who had flown into WA had tested negative.
"We're not out of the woods on that one yet," he said.
Three mine workers who had returned to Tasmania are in quarantine and have reportedly tested negative.
Newmont Australia said it was continuing to work closely with the NT Department of Health to respond to the detection of COVID cases.
"Newmont's first priority is to protect the health and safety of our workforce, and our communities," the company said today.
"The Tanami operation remains shut down, with people isolating in individual rooms except for those responsible for critical operations such as catering and support services."
The NT government has deployed a response team to site, and Newmont is implementing any further actions as directed.
"Newmont is mobilising additional external resources to Tanami to assist with support services, as our focus is on the health and safety of our workforce and particularly those currently isolating on site," the company said.
"Newmont is also in close contact with other state governments to assist with any required information to support contract tracing and testing of those approximately 800 individuals who have left site since the 18th June 2021."