The male driver was taken to hospital with head and arm injuries after the tree smashed into his cab near Glencarse, east of Perth, just after 4.45pm on May 21.
He hit the emergency brake when he saw the branches across the line, which slowed the train from 74mph to 63mph before the collision seven seconds later.
The 28 passengers and conductor on the Perth-Dundee service escaped injury but the “outer skin” of two of the windows of the carriages were broken.
However, Network Rail was unable to establish who was responsible for maintaining trees at the site despite finding several in a hazardous condition in an inspection last September, The UK Department for Transport’s rail accident investigation branch (RAIB) revealed today.
They are on a narrow strip of land between the rail line and a slip road on the A90 Perth-Aberdeen trunk road, and are thought to have been planted when the junction was built in 1973 to reduce road noise to nearby houses.
The RAIB report said it was not clear from the inspection report whether the Monterey cypress which fell was specifically identified.
It said the Network Rail inspection “identified that there were various lineside trees on that section which presented a high risk to the railway, such that the owners should be notified of the inspection findings and the area re-inspected within one year.
“Network Rail attempted to establish if a contractor was responsible for managing that area of land, which is owned by Scottish ministers, but it was not able to do so and no action to make the trees safe was taken before the accident occurred in May.
"[Scottish Government agency] Transport Scotland has stated that the land from which the tree fell is outside the boundary of the trunk road network that it manages, and it has been unable to identify anyone who is responsible for managing the land.
"Following the accident, Transport Scotland has instructed the company which operates the trunk road network on its behalf to inspect the area and do what is necessary to make the land safe, including the removal of any further trees that may be an issue.”
The RAIB report said the branches had fallen after the previous train had passed an hour earlier.
The weather had been dry with light winds and there was “no evidence the branches fell due to the direct effect of abnormal weather”.
The report said the incident “demonstrates the importance of railway authorities and owners of adjacent land having arrangements in place to manage the risk from potentially hazardous trees, including being aware of the condition of trees which may pose a risk to the safety of the railway, and taking action to manage the risk.”
A Transport Scotland spokesperson said: "Whilst the area from which the tree fell is not part of the trunk road network, we have instructed our maintenance contractor to inspect the area and take whatever action is required to make it safe so as not to unduly delay this essential work while further details are established.”
Kevin Lindsay, organiser in Scotland for train drivers’ union Aslef, said: “It’s not acceptable that neither Network Rail nor Transport Scotland have taken responsibility for maintaining land and vegetation near or on railway land.
"The sad fact is this failure resulted in injury to the train driver.
"It’s time for Graeme Dey, the transport minister, to get a grip of his brief as his inaction is having detrimental on Scotland’s railway.”
A Network Rail Scotland spokesperson said: “This incident highlights how overgrown or diseased third-party trees and vegetation pose a safety risk to our railway.
"We work closely with landowners along our railway to identify and remove dangerous trees and have a £25 million, five-year vegetation management programme aimed at reducing incidents such as this one.
"Following this accident, we carried out extensive works to remove third-party trees at this location and other points on the line.”