Nyrstar's Port Pirie Smelter will breach conditions of its new licence at the end of the year, based on current tracking of lead emissions, South Australia's Environment Protection Authority says.
Nyrstar's licence for operations at Port Pirie was renewed in July and included tougher lead in-air limits and targets.
EPA chief executive Tony Circelli says based on current readings Nyrstar will exceed its new annual average lead-in-air limit on December 31.
"Once this is confirmed, Nyrstar will be in breach of its new licence and this will trigger a formal EPA investigation," Mr Circelli said.
"Nyrstar will be required to provide a report to the EPA by January 8 detailing the cause of these targets being exceeded, and actions it proposes to take.
"Based on that information, and the EPA's own investigation, we will then determine what further enforcement actions are appropriate."
When it renewed the company's licence, the EPA applied significantly tighter conditions effectively requiring a 20 per cent reduction in emissions.
Mr Circelli said the EPA considered the new conditions to be reasonable and practically achievable and important to drive improved environmental performance and accountability.
"Breaching licence conditions is a serious matter and ultimately, Nyrstar is responsible for meeting the conditions of its EPA licence, including lead-in-air limits and targets imposed to protect the environment and human health," he said.
"While the EPA investigates this matter formally, it will not be appropriate to comment or speculate on likely compliance outcomes.
"Suffice to say, this is an extremely disappointing outcome and indicates unacceptable discharges of lead to Port Pirie in 2020."
Nyrstar said the reduction of lead emissions was a key focus for the company.
It recently outlined a number of projects designed to reduce emissions including installation of a new environmental hopper on the wharf to reduce emissions generated by loading and unloading activities and an upgraded wheel wash for all vehicles leaving the site to reduce the transmission of contaminated lead-bearing material.
"Management of air quality is a priority for Nyrstar as a key environmental aspect requiring ongoing operational monitoring and management to ensure Nyrstar continues to meet its legal obligations, expectations of the community and corporate quality standards," the company said on its website.