In a statement, the Australian Transport Safety Bureau (ATSB) said: "The driver alighted from the locomotive to inspect an issue with a wagon".
The driver had stopped at Hesta Siding to check a wagon, but the train - en route from Newman to Port Hedland - took off without him and careered 92 kilometres down the track before being derailed at Turner Siding. The engineer had left the locomotive to inspect an issue with an ore auto, and the train then began moving.
The train had four locomotives and 268 wagons, the ATSB said.
It was deliberately derailed at a set of points, operated by a control centre, about 119km from Port Hedland.
A train with no-one on board travelled at 100km/h for 92km in a remote area of Australia before being deliberately derailed. It averaged about 68 miles per hour and traveled for some 50 minutes before it was derailed, according to Australia's ABC.
"We can not speculate on the outcome of the investigation, however we are working with the appropriate authorities and our focus remains on the safe recovery of our operations", the BHP spokeswoman said.More news: FA appeals against decision to clear José Mourinho over touchline language
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WA Premier Mark McGowan said he had not been briefed on what happened but it would have been very concerning for everyone involved.
BHP's rail operations in Western Australia have now been suspended.
"Usually, once the driver leaves the train, the brakes are on, there's procedures for that", Rail Safety Consulting Australia owner Phillip Barker told ABC.
The MySteel 62% Australian fines iron ore price has been stronger-than-expected in recent weeks at above US$70 per tonne, rising above $77/t late last month.
"Investors are keeping one eye on the developments in the Pilbara after BHP announced it had halted all rail operations", ANZ bank said in a report.
The Rio Tinto company says it completed its first delivery of iron ore using an autonomous train in July.