"They have obviously defamed her," Johnny Nadérus of the Seko union said to the Svenska Dagbladet daily on Sunday.
The cleaner was initially given the blame for the crash in the early hours of Tuesday morning which left a Saltsjöbanan train embedded in the side of a house in the suburb of Saltsjöbaden in eastern Stockholm.
"She was a cleaner. Somehow she managed to get in and steal one of the trains. We're investigating how it could have happened," Tomas Hedenius, a spokesman for the rail operator Arriva, told the Aftonbladet daily on Tuesday.
However on Friday investigators confirmed there was no reason to believe that she intentionally drove off in the train.
The investigation is now instead looking at whether the crash was a crime against Sweden's workplace safety laws in order to assess what responsibility the train operator had in causing the accident.
Tomas Hedenius on Friday expressed regret for how the story had developed.
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"I made it 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," Hedenius told The Local.
"I should have done more to make it clear that there are several possible scenarios. Obviously I didn't do it enough.”
The Seko union intends to take a decision on Monday whether to press charges against Arriva.