Dikshit's comments came hours after Rushdie's planned video address at the Jaipur Literature Festival was cancelled at the last minute over fears of violence following protests by Muslim groups.
Earlier in the day, Dikshit had indicated that the writer was welcome in the city.
"We welcome everyone. We don't want to get into all this. He is a very well known writer and there may be differences in opinion over what he writes. He is a very very eminent writer," she told reporters on the sidelines of a function in New Delhi.