On Wednesday morning, only one track was in use between the central station and the Stockholm South station and commuter trains were expected to run at reduced capacity between the two stations for another week.
There were also delays, rerouting and cancellations on other train routes.
"It can take seven to ten days to repair the damages," Lena Enghardt, a spokesman for the Swedish Transport Administration (Trafikverket), told Radio Sweden.
"The situation is more or less what we expected. Trains passing Stockholm South will have minor delays and we are redirecting and rerouting trains in Flemingsberg," said Anders Edgren, a spokesman for the SJ national rail operator.
The train troubles could also affect road traffic in the Stockholm area, with longer queues than usual expected on Wednesday
One commuter, Emil Dangaard from the Stockholm suburb of Lidingö, said he was impressed by the service on Wednesday morning.
"I was here in good time and received good information...I haven't experienced any big problems," Dangaard said.