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"We just have a skeletal team to run the mine," PT Freeport Indonesia spokesman Riza Pratama told Reuters.
He did not tell the wire service how many workers would remain, how many had tested positive nor how many were being kept in isolation.
The operation has a workforce of more than 25,000 employees and contractors.
The head of the company's office in Jayapura, Anderson Warobai, had told local media earlier this month 52 employees had tested positive for COVID-19.
"We are pleased to see positive cases responding well to treatment, with many on the road to full recovery," PTFI president director Tony Wenas said in a statement last week.
In the update, PTFI said it was strengthening its health care system in response to the pandemic, increasing testing, providing additional medical personnel and increasing the number of isolation accommodations.
It had expanded its dedicated isolation facilities to accommodate more than 750 people in Tembagapura and 150 people in the Lowlands at Mile 38.
It said this included additional dormitories at the PTFI Mimika sport complex, which the public health authority had converted into isolation accommodation for the Timika community.
"The existing health facilities and number of medical personnel in Tembagapura and Kuala Kencana are sufficient to handle anticipated scenarios," International SOS chief medical officer Dr Darma Irawan said at the time.
COVID-19 cases had reached 150 on Sunday in the Mimika regency, where Grasberg is located, and three deaths, Reuters said.
Indonesia has more than 18,000 confirmed COVID-19 cases and 1,191 deaths, according to Johns Hopkins University today.