MinRes and Arc Infrastructure said the train derailed early on Sunday morning, south of Norseman, as it was returning to the mine from Esperance.
Around 30 empty iron ore wagons derailed. The train comprised 106 wagons. There was damage to some of the wagons, but not MinRes' locomotives and no one was injured.
It was the second iron ore train to derail in Western Australia in just six days, following BHP's forced derailment last Monday.
MinRes said initial investigations into the incident indicated all safe train operating procedures were followed at all times, but a full investigation is underway.
At this stage, it appears localised heavy rains and flash flooding washed out some ballast from under a small section of the track.
MinRes is working with Arc, the owner and operator of the track, to assess the damage and how long repairs will take, but it is expected to open within days. The company does not expect the incident to have a material impact on Koolyanobbing.
MinRes managing director Chris Ellison said haulage would be resumed once the company received confirmation the track was repaired.
"Most importantly, no one was injured," he said. "Mineral Resources continually reviews its operating procedures to ensure we maintain a safe work place and achieve our safety objectives."
The train left Koolyanobbing on November 7, carrying the maiden load of 7,488t of iron ore fines since MinRes acquired the mine from Cleveland-Cliffs three months ago.
The company will start stockpiling ore at the port ahead of the first shipment, expected within four weeks.
Koolyanobbing produced 92,000t of iron ore in the September quarter. MinRes expects the mine to produce 6-6.25 million tonnes of iron ore per annum.