The revelation came as the minister said the line would remain closed “into October”, confirming a Scotsman story last week that it would stay shut for at least another month following the 12 August incident.
Mr Matheson told the Scottish Parliament’s rural economy and connectivity committee the change in Network Rail procedure was included in the track body’s interim report on landslip risks.
It was submitted yesterday to the UK Government, which is responsible for rail safety.
Mr Matheson said: “They [Network Rail] have already changed some of their protocols for decision-making during periods of adverse weather.
"I would probably categorise that as they have implemented changes which would take a more cautious approach when periods of adverse weather take place.
"That has already been issued to staff.”
It is understood the new procedures involve extra checks and monitoring in at-risk areas before and during bad weather, such as to tracks, drainage culverts and bridges over rivers when heavy rain is forecast.
A Network Rail spokesperson said later: “We have introduced additional processes ahead of forecast periods of extreme rainfall to further enhance how we prepare for, and respond to, these weather events.”
Driver Brett McCullough, 45, conductor Donald Dinnie, 58, and passenger Christopher Stuchbury, 62, died when the 6:38am Aberdeen to Glasgow Queen Street train crashed into a landslide across the tracks at Carmont, south of Stonehaven, following heavy rain.
An interim report by the UK Department for Transport’s rail accident investigation branch revealed the train which derailed was travelling at nearly 73mph, just under the 75mph speed limit for that section of the line.
It is understood that train drivers operate under instruction from Network Rail signallers over any changes to speeds.
However, the procedure changes are believed not to affect such operations, which are already governed by rules, such as trains being slowed down or stopped when tracks are flooded.
A separate investigation has been launched by British Transport Police and Police Scotland.
Mr Matheson said a new access road to the crash site was being built so the wrecked carriages could be removed.
He said it had involved “significant” work, which was now at a “very advanced stage”.
He said: “Once that is complete and once the investigations are complete, Network Rail will be in a position to start the recovery phase.
"My expectation is the line will remain closed for passenger use into October given the scale of the challenge.”
ScotRail introduced a train shuttle service between Aberdeen and Stonehaven on Monday but buses are still replacing trains between Stonehaven and Dundee.
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