Driver Brett McCullough, conductor Donald Dinnie and passenger Christopher Stuchbury were killed in the accident.
Michael Matheson highlighted the "very intense rainfall" in the area and said an increasing number of weather events are impacting the rail network.
The driver, conductor and a passenger have died.
"Its detection is proof that our surveillance system is doing its job."
Olivia Nalwanga and her two-week-old son Zeus were last seen on Saturday.
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