The cleaner was suspected of intentionally driving the train off its tracks and into the house Tuesday, Sweden's TT news agency reported.
"There's no longer reason to suspect her of any crime," prosecutor Par Andersson said.
Both Stockholm public transit operator SL and subcontractor Arriva hinted the cleaner, whose name was not released, took control of the train before it crashed through a barrier at the end of the line.
"I made clear from the beginning that all scenarios were possible. It's unfortunate that she was depicted as a thief, and I'm truly sad about that," Tomas Hedenius, a spokesman Arriva, told TheLocal.se.
Andersson said "unfortunate circumstances" allowed the woman to put the train in motion.
"The forensic investigation showed that there were a number of serious safety breaches on the train and where it was parked," the prosecutor's office said in a statement.
The investigation is now focusing on whether workplace safety laws were violated during the incident, officials said.
"If the investigation shows that there were workplace safety violations and there is a connection with what happened, that could be grounds for suspicions that a workplace safety crime has taken place," prosecutor Mats Palm told TT