National Public Radio will continue for now to refer to Private Manning as “he,” according to a spokeswoman, Anna Bross. “Until Bradley Manning’s desire to have his gender changed actually physically happens, we will be using male-related pronouns to identify him,” she said.

Rich Ferraro, a spokesman for Glaad, a gay-rights group, said he had been reaching out to news organizations to change their usage. He noted that nearly every major style guide says the media should use the pronoun preferred by the subject. “All of the media coverage today shows how far behind the media is covering transgender people,” said Mr. Ferraro.

The New York Times stylebook guides writers typically to refer to a subject the way he or she prefers. But Dean Baquet, the managing editor of The Times, said in an e-mail: “Generally speaking we call people by their new name when they ask us to, and when they actually begin their new lives. In this case we made the judgment readers would be totally confused if we turned on a dime overnight and changed the name and gender of a person in the middle of a major running news story. That’s not a political decision. It is one aimed at our primary constituency — our readers.”

In a blog post, The Times’s public editor, Margaret Sullivan, encouraged The Times to change how it refers to Private Manning. “It may be best to quickly change to the feminine and to explain that — rather than the other way around,” she wrote.

Some news outlets, like The Huffington Post, did follow Private Manning’s wishes. New York magazine, which also referred to Private Manning as “she,” had an answer to why there has been such a fuss: readers’ squeamishness and the divided feelings toward Private Manning. “What’s the worst that could happen?” it wrote. “She changes her mind and we go back to he? Even the worst-case scenario is so minor it doesn’t qualify as a problem.”