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The South East Asian country went into lockdown almost a week ago under an official Restricted Movement Order in a preventative measure to control the outbreak, with the order scheduled to end on March 31.
Under the RMO all industries must restrict their movements except those that are part of the supply chain of essential goods.
This includes oil and gas, petrochemicals, fertilisers and pesticides and some electrical products.
Lynas told the market it supported the government's actions and had accordingly shut down the plant and gone into care and maintenance mode, with all staff to be paid during the shutdown.
The company said operations at Mt Weld in Western Australia would continue as normal.
With the plant pumping out good volumes through March Lynas said it was in a good cash position to handle the shutdown.
The company had $111.8 million in the bank in December.