“The woman started driving the train from the Neglinge train station, which is two stops from Saltsjöbaden, and usually a three-minute ride,” SL spokesman Jesper Pettersson told The Local.
"The train usually goes at about 10 kilometres an hour in this area, but we estimate that she was going at about 70 kilometres per hour."
When the train reached the final stop on the line at around 3am, it careened off the tracks and into the first-floor kitchen of one of the house's three flats, causing severe damage.
No passengers were on the train at the time, but a woman was trapped in the wreckage for two hours before rescue crews managed to get her out.
“We still don’t know why she was in the driver’s seat or whether the incident was an accident. There’s a police investigation underway and we’re waiting for them for clarification.”
The cleaner, who is in her twenties, was flown by helicopter to the Karolinska University Hospital for treatment of what emergency workers described as "serious" injuries.
She has since been ordered detained on suspicion of public devastation (allmänfarlig ödeläggelse).
RELATED PHOTO GALLERY: More images from the scene of the crash
According to the Expressen newspaper, there were five residents from three different families sleeping in the building at the time of the accident.
"It's incredibly lucky that no one in the house was injured," police spokesman Ulf Lindgren told the TT news agency.
"The head of the emergency services crew has ordered the house to be evacuated for safety reasons."
As of 1.30pm, the derailed train was still inside the house, according to Pettersson, while emergency services determine how to remove it.
“It’s important to find out if the structure of the house can cope with the removal of the train, no one wants to risk the building’s integrity,” he told The Local.
A spokesman for subcontractor Arriva, which is responsible for operating the line, characterized the incident as a theft.
"It was a cleaner who for unknown reasons stole the train," Arriva spokesman Tomas Hedenius told Aftonbladet.
"She was a cleaner. Somehow she managed to get in and steal one of the trains. We're investigating how it could have happened."
In the wake of the incident, local politicians have called upon SL to beef up security procedures.
"It shouldn't be possible for unauthorized people to drive our trains," Christer G Wennerholm, a Moderate member of the Stockholm County Council's traffic committee, said in a statement.
Replacement buses are taking commuters between the Neglinge and Saltsjöbaden stops on the Saltsjöbanan train line, according to SL, although the rest of the line is functioning normally.
Jesper Pettersson at SL promised the incident will result in a "major review" of the company's current security system.
Follow The Local on Twitter