The Perth to Dundee service hit the fallen tree at 4.47pm on Friday May 21 near Glencarse, the UK Government’s rail accident investigation branch (RAIB) announced.
It said: “The tree penetrated the windscreen, causing injuries to the driver and damage to the cab.”
ScotRail declined to provide any further details.
The RAIB added in a brief update on the crash: “We have undertaken a preliminary examination into the circumstances surrounding this incident.
"Having assessed the evidence which has been gathered to date, we have decided to publish a safety digest.
“The safety digest will be made available on our website in the next few weeks.”
None of the passengers on the train were understood to be injured, with paramedics checking the carriages.
One passenger praised ScotRail staff on the train for doing an “amazing job”.