The Mining and Energy Union says rail workers were left "shaken" and narrowly escaped harm when the train they were repairing was struck by another in Western Australia's Pilbara region.

Mining giant Rio Tinto said an autonomous train hit a set of stationary wagons about 80 kilometres outside Karratha just after midnight on Monday, damaging 22 wagons and three locomotives.

A Rio Tinto spokesperson said no people were in the vicinity and no-one was injured, but union secretary Greg Busson said five staff were further down the line working on the stationary equipment.

Iron ore trains can be several kilometres long and Mr Busson confirmed the group were unharmed, but said they were shaken by the incident.

He said if workers were closer to the site of the crash the consequences could have been far more serious.

"[They were working] in the dark in an isolated area, and even though they were a bit away from where the incident happened they were still at risk and it's obviously shaken them," he said.

The Office of the National Rail Safety Regulator (ONRSR) has launched an investigation and yesterday said it received a report about a collision between a loaded ore train and a recovery train.

"The recovery train is reported to have collided with the ore train it was sent to recover after it was disabled by a mechanical failure," a spokesman said in a statement.

The spokesman said in its early stages the investigation would focus on the operation of and adherence to signalling systems in the area.

Mr Busson said the workers were undertaking a "train rescue" on the equipment that had failed and only escaped harm after a mayday signal was issued minutes before the crash occurred.