The train hopped off the tracks early Tuesday morning between Stuvsta and Huddinge, south of Stockholm.
"It felt like an earthquake," witness Göte Larsson, who lives just 20 metres from the scene of the accident, told the TT news agency. "The entire building vibrated and my bed shook."
"At first I couldn't see anything when I looked outside, but then I saw how the train went off the tracks."
The derailment started at a switching system about 200 metres from where the train came to rest. The tracks just past the switch were left twisted.
"Around 350 metres of track are severely damaged," Tomas Borg of the Swedish Transport Administration (Trafikverket) told TT.
Borg added that it was "too early" to speculate on what might have caused the derailment, but the agency estimated that repairs could take up to a week, causing problems for both national passenger trains and commuter trains, as well as cargo trains.
Some trains in and out of Stockholm would be redirected, resulting in delays of up to an hour, while some local train departures stand to be cancelled altogether. National rail operator SJ announced on Tuesday that the accident would result in all trains between Stockholm and Gothenburg being rerouted through Västerås, delaying arrivals by about an hour.
"Any train that passes the accident site can expect a half-hour delay. But it can be longer during certain times of the day, but I don't want to speculate on exactly how long," SJ spokesman Ronny Hörstrand told TT.
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Some regional trains might also be cancelled, he added.
The derailment was the second in the Stockholm region in recent months. In November, a cargo train went off the rails in central Stockholm, just north of Södra Station, causing weeks of delays.
Borg with the Transport Administration called the two recent derailments a "coincidence", emphasizing once again that "it's too early to speculate what caused this derailment".