Many commuters were left stranded on Wednesday morning after the fault, which saw train traffic heading north from Stockholm affected. Trains heading to Uppsala and beyond, as well as the Arlanda Express to the airport, were all cancelled.
"There are truly a lot of passengers in these areas," Tomas Borg at the Swedish Transport Administration (Trafikverket) told the TT news agency.
Another spokesperson said the problem could last "at least to the end of the day". The fault was caused by a fire at the Myrbacken station, which damaged electric cables.
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Passengers have been asked to take replacement buses.