Due to the heat and the risk of so-called sun curves on the tracks, train traffic is being cancelled in Kalmar County, Östergötland and Värmland, among others, until Monday morning.
Which routes are affected can change quickly, according to the Swedish Transportation Authority, which advises travellers to keep an eye on their website.
In addition, Thursday's derailment in Bollebygd will affect train services between Stockholm and Gothenburg for over a week.
On Thursday afternoon, about ten carriages in a 600-metre-long freight train derailed in the municipality of Bollebygd between Gothenburg and Borås. It is thought that the derailment was caused by "sun curves," which refers to the heat from a hot sun bending or expanding railway tracks.
The accident has had a major impact and on Friday morning a few SJ trains from Gothenburg were rerouted via Öxnered. The other trains are running from Stockholm to and from Borås or Alingsås, with replacement buses to Gothenburg on the last leg.
Train traffic between Gothenburg and Kalmar is also affected. SJ is collaborating with Västtrafik so that passengers can travel on Västtrafik buses from Borås.
"The same arrangement will be in place this weekend and probably also Monday to Sunday next week," said Peter Kraméus from SJ's press office.
Four departures from Stockholm are being cancelled due to a shortage of vehicles that has arisen as a result of the accident. Otherwise, SJ expects the journeys to run as normal – but take longer.
"We are running 22 trains today between Gothenburg and Stockholm. All will arrive, but it will probably take a little longer than usual," said Kraméus.
According to the Swedish Transportation Authority, it may take at least until next weekend to completely clear and restore the accident area.
"You need to remove some trees, build a temporary road and a ramp before you can lift the carriages that are in the worst condition," said Denny Josefsson, press communicator at the Swedish Transportation Authority.
"I have been told that twelve carriages have derailed. It looks like it could take the whole of next week too," Josefsson continued.
The derailment is believed to be due to a so-called sun curve about which the train driver had raised an alarm about just hours before the accident, local media reports.
A section was examined without finding any faults, less than an hour before the derailment occurred a few hundred meters further away.
"We are all upset," said Hanna Ekberg, section manager at the Swedish Transportation Authority, to SVT News West.
"We don't know if we missed it, but it will have to be investigated. It is not impossible that there has been another [sun curve]. These are incredibly unfortunate circumstances."