The train crossed the Lamington viaduct in South Lanarkshire, which carries the West Coast Main Line over the River Clyde, after it was undermined by spate waters at Hogmanay.
The Rail Accident Investigation Branch (RAIB) has announced it will investigate what it described as a “dangerous occurrence.”
The viaduct is still closed for emergency repairs.
The incident took place on the same day the damage occurred, before a decision was made to close the line.
Investigators said the driver of a Virgin West Coast service from Edinburgh Waverley to London Euston reported a potential problem at 7:35am on 31 December, saying there was a dip in the track after the area was hit by torrential rains from Storm Frank.
In response, signallers restricted the speed of trains on the section of the line affected. Maintenance staff inspected the track and watched a southbound train pass over it at low speed.
They then decided that it was safe to lift the speed restriction.
But when a northbound train crossed the viaduct at high speed at 8:40am they noticed “unusual track movement”.
That prompted them to immediately re-impose the speed restriction.
A few minutes later, at 8:57am, they closed the line to all trains after finding a large crack in one of the concrete piers supporting the viaduct.
A more detailed investigation has since found a large hole beneath the pier, along with subsidence and damage to three of the steel bearings which support the bridge deck.
After the closure of the line on 10 January, a disused part of another pier under the viaduct collapsed. Bridges over rivers can be liable to “scour damage”, where fierce currents undermine the structure.
A spokesman for Network Rail said: “The safety of passengers and our workforce is of vital importance and we are already conducting our own internal review of the incident at Lamington.
“We will work closely with the RAIB as it completes its inquiry.”
Engineers said last week that they expect the West Coast Main Line to remain closed at Lamington Viaduct until the beginning of March while repairs are carried out.