OEFA first said last weekend that it has seen a "greenish solution" flowing from the mine into a local river, and said it would provide into a potential tailings spill at the copper-molybdenum project outside Lima.
"[We have] verified that there was no tailings spillage towards the zone of tunnel R1, in the annex of Tala, district of Torata, province of Mariscal Nieto, in the department of Moquegua," the agency said.
"The supervisors of the OEFA verified that the concrete channel of the mining unit that was conducting tailings was not affected. However, solid material dragged towards the Charaque stream was found."
OEFA is now processing several sediment samples to determine the material's content.
Southern Copper denied any tailings spill to Reuters, but reportedly noted that the rains caused flooding at some installations and one of its workers was swept away in a mudslide.
Cuajone's concentrator plant, according to the news service, is currently suspended but it should be brought back online in the coming days.
Cuajone is made up of an open-pit copper mine and concentrator and first commenced production in 1976.