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There were some 1306 cases of COVID-19 recorded in Malaysia, and 10 deaths.
Lynas said it had taken the steps to initiate a safe temporary shutdown of its plant into care and maintenance mode.
It has retained some work-in-progress inventory and believes it will be able to ramp up quickly once it can restart.
The Mount Weld mine in Western Australia was expected to continue to operate.
"We have taken actions to significantly reduce cash outgoings during the temporary shutdown," Lynas said.
The rare earth producer said its plant had delivered strong production during the March quarter to date, and it was in a strong position to avoid a significant majority of costs under the shutdown scenario.
Lynas expects to achieve positive cashflow from operations during the March quarter, before payment of A$14 million relating to the permanent disposal facility project.
It had $111.8 million in cash at December 31.
Lynas shares dropped 14% on the news to $1.09, valuing the company at $763 million.