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Implats confirmed it faced charges for allegedly contravening the lockdown rules, having urged workers to return earlier last week which had prompted unions to voice concerns.
Local media reported some recalled workers had been turned back by police.
Impala Rustenburg CEO Mark Munroe faced court on Friday representing the company and the matter has been postponed for further investigation.
"Impala has to date, and continues to, undertake its operations in a legally compliant and responsible manner," the company said in a statement.
Resources minister Gwede Mantashe announced the amendments to the lockdown regulations for the mining and energy sectors on Thursday.
The move follows the Minerals Council South Africa warning last week up to 45,000 jobs could be at risk if the lockdown to curb the COVID-19 pandemic was "prolonged".
Mantashe said mines, excluding collieries supplying Eskom which had been allowed to continue to ensure power generation, could operate at the reduced capacity of 50% during the lockdown "and thereafter at increasing capacity as determined by the cabinet member responsible".
"We are proactively managing issues directly affecting the industries, in the interests of ensuring employee health and safety, as well as ensuring that these sectors are able to meet their obligations," he said.
The government said miners must implement a rigorous screening and testing programme as employees returned to work, provide quarantine facilities for workers who tested positive for COVID-19 and make arrangements to transport employees from their homes to their areas of operations.
It also said workers from neighbouring countries would be recalled at the end of the lockdown, which has been extended from April 16 to April 30.
The Minerals Council has welcomed "the spirit of the amendments".
"It is Minerals Council's view that government has adopted a pragmatic and practical approach to fighting the pandemic and enabling the economy to survive the crisis," CEO Roger Baxter said.