The Caledonian Sleeper train was stopped using an emergency brake after overshooting the platform at Edinburgh Waverley.
The Northbound Lowlander service ended up several hundred yards to the east of the station after the incident on Thursday.
Operator Serco confirmed the train’s manager deployed the emergency brake.
The company said its own investigation had revealed the incident was the result of an “operational mistake”.
An inspector from the Rail Accident Investigation Branch was sent to the scene to gather evidence.
The train blocked a junction, halting trains to and from North Berwick, Dunbar, Tweedbank and London.
TSSA union general secretary Manuel Cortes said: “Clearly this is an incredibly serious situation which calls for nothing less than the grounding of the entire new Sleeper fleet until we have the full details of the what went wrong.
“No one should be playing fast and loose with faulty brakes on our railways and Serco need to wake up to that fact and act now.”
Ryan Flaherty, Serco’s managing director for Caledonian Sleeper, said: “We are very proud of our train manager who followed the correct processes and deployed the emergency brake to bring the train to a stop during yesterday’s incident at Edinburgh Waverley.
“Our own early investigation indicates there are no technical or safety concerns with the rolling stock and that this was an isolated operational mistake.
“Following the incident, our new trains ran as normal last night and will do so again this evening.
“We will continue to work with the relevant authorities to investigate the underlying cause and expect to provide an update next week.”
A Rail Accident Investigation Branch (RAIB) spokesman said: “An RAIB inspector was deployed yesterday to gather evidence. We will use this information to decide any further course of action.”
The Sleeper service has been besieged with problems since its re-launch and staff recently voted for industrial action in a dispute over “appalling” working conditions.