The alarm came in at around 11:30 PM on Monday when the driver of an X2000 train carrying several hundred passengers passed the location in the suburb of Huddinge where the accident later took place.
Two calls came in from the driver who said he had a heard a "damn big bang". He said: "I'm afraid it could be the actual switch so you have to inspect that carefully."
Reporters from Swedish Television heard the drivers' phone messages and found that the Transport Administration only sent out service staff at 12:35 AM on Tuesday, after the driver of the freight train had reported that his train had derailed.
The Transport Administration's own rules say that "traffic should be stopped as soon as possible" when either people, the environment or property are at risk.
"This sounds like such an occasion when one should at least notify the driver of the next passing train to slow down and to be cautious," Claes Elgemyr of the Transport Administration told Swedish Television.
"The decision to send people out there shows that one had in fact deemed something to be wrong and so one should have ensured that the next train passed carefully."
Maria Nichani, also of the Transport Administration, said that an inquiry is ongoing.
The Seko union said that they have pointed out problems with the railroad switch 43 times since 2008, including reports from inspectors who have said it was ruined by rust. Seko now wants the Transport Administration's CEO Gunnar Malm to step down.