The incident happened near Dalwhinnie station at around 0315 on Saturday, 10 April, during overnight testing.
It was not a passenger service, and nobody was injured during the incident, Scotrail has confirmed.
Regulators The Rail Accident Investigation Branch said on social media: “RAIB is deploying inspectors to gather evidence following the derailment. The train consisted of a short-form HST that was travelling south when the last two vehicles derailed in proximity to points.”
Passengers were notified early this morning that services between Perth and Inverness had been halted. Scotrail has warned passengers of ongoing disruption and to check for updates before travel.
Currently north-bound trains are going to Pitlochry and restarting from Aviemore, while south-bound services are stopping at Aviemore and starting again at Pitlochry.
Bus replacements are operating at all stations between Aviemore & Pitlochry.
It is not yet known how long the process will take to recover the train and reopen the line but Network Rail said they will provide updates via their social media.
A ScotRail spokesperson said: “Services between Perth and Inverness are currently disrupted, there will be replacement bus services for those making essential journeys.
“Customers should check our website, app and social media channels for the latest arrangements before they travel.”
A Network Rail spokesperson said: “Engineers are on site to get services back up as soon as possible. We apologise to customers for the disruption to their journeys.”