Mayor Thomas M. Menino won’t back down from his stance against Chick-fil-A, but he acknowledged Thursday that he cannot do anything to prevent the restaurant chain from setting up shop in Boston.

“Originally, I said I would do everything I can to stop them. And that was mostly using the bully pulpit of being mayor of the city and getting public support,” Menino said in an interview at City Hall. “But I didn’t say I would not allow them to go for permits or anything like that. I just said we would do everything we can, bully-pulpit wise.”

Menino caused a stir last week when he wrote an ireful letter to the restaurant chain’s president, Dan Cathy, who told the Baptist Press this month that his company is ‘‘guilty as charged’’ as a supporter of organizations rallying against same-sex marriage.

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The company was considering opening a location on Union Street, across the street from City Hall and from Faneuil Hall. After learning about the company leadership’s anti-gay views, Menino issued a letter to Cathy, lambasting the president’s view.

“I was angry to learn on the heels of your prejudiced statements about your search for a site to locate in Boston,” Menino wrote. “There is no place for discrimination on Boston’s Freedom Trail and no place for your company alongside it.

“I urge you to back out of your plans to locate in Boston,” Menino said.

The letter drew intense reactions on both ends of the political spectrum. Since it was posted on the city’s Facebook page Wednesday, about 140,000 people have “liked” it.

But Thursday, Menino clarified his view, saying that it would not be within his power to take any steps to prevent the business from establishing a franchise in the city and he could not deny permits to the company. His only recourse, he said, is expressing his disapproval.

“Yes, people have criticized me, I understand that,” Menino said. “But I have feelings ... I have my First Amendment rights also. I’m expressing them.”