Romson, of the Green Party, made the comment today on public television while talking about fellow party member Mehmet Kaplan's resignation as housing minister a day earlier.
Romson said when Kaplan was the chairman of a Muslim youth organization he faced difficult situations "like the September 11 accidents and such."
Asked to explain her choice of words, Romson condemned the attacks and told Swedish newspaper Aftonbladet she meant they brought misfortune to Swedish Muslims.
The word for misfortune and accident is the same in Swedish.