The 1,000 km (620 mile) rail line is used by miners including Glencore, MMG Ltd and South 32 to carry zinc and lead concentrate from the Mt Isa region.
Peru's environmental regulator OEFA has concluded that mining waste from the company's Cuajone mine did not spill into a river during heavy rains last week.
The country's environmental agency OEFA detected a "flow of a greenish solution" into the nearby Torata River in the waste deposit area of the copper mine, located in the Moquegua region.
