In a suit filed with the Labour Court, the ombudsman is demanding the company pay 120,000 kronor ($18,500) in damages.
The woman was hired in October 2007 to work as a cleaner for the company, which is based in Anderstorp in southern Sweden.
But after working for only a few days, the woman was let go.
The company claimed she was fired because her choice of clothing, a long skirt, made it impossible for her to continue with the job.
According to the company, working as a cleaner requires that one wear long pants.
The woman said she was not informed about the clothing regulations and that she wore the skirt because of her religion.
According to Eva Hagström, a lawyer from the ombudsman’s office, the incident is just one of many in which Muslim women are discriminated against on account of their clothing.
“These women encounter problems in both their professional life and in connection with everyday activities. It’s an ongoing discrimination which shuts these women out and that is something we can’t accept,” she said in a statement.