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The watchdog has filed nine charges, according to SMA documents.
This is the second time Los Pelambres (pictured) has been charged by SMA. In 2013 the regulator charged the copper mine for breaching conditions concerning the archeological heritage of the area in which it operates.
The new charges include extracting water from three wells from which SMA could not verify it had the permits to do so, construction of seven unauthorized water wells, delivering reports without all of the required information, and failure to reforest some areas.
Of the nine breaches, five are classed as "serious" and four "minor." As a result, the company is facing fines that could total 29,000 UTAs (annual tax units, some US$23.9mn), the revocation of its RCA or the temporary or permanent closure of its facilities.
Antofagasta, in a statement, said it had not been officially notified by the authorities, noting that it is implementing a series of plans to fully meet its environmental commitments.
Los Pelambres invests about US$40mn a year in the area of sustainability, company chairman Francisco Veloso said.
Los Pelambres, in central-northern region Coquimbo (IV), produced 375,800t of copper in 2015, the equivalent of 6.5% of Chile's copper output. Production between January and August this year was 237,300t, according to Chile's copper commission Cochilco.
Antofagasta Minerals is controlled by London-listed Antofagasta plc, the mining arm of Chile's Luksic group.