WASHINGTON — The Obama administration has inserted language into the federal jobs Web site explicitly banning employment discrimination based on gender identity.

The protection is expected to apply to the small transgender population — people who identify their gender differently from the information on their birth certificates — and it merely formalizes what had been increasingly unchallenged government practice over several years.

But civil liberties and gender rights groups welcomed it on Tuesday as the clearest statement yet by the Obama administration that such discrimination in the federal workplace would not be accepted.

Mara Keisling, executive director of the National Center for Transgender Equality, said, “The largest employer in the country is doing what all the other large employers in the country are doing, so that’s really great news.”

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But the new standard brought instant criticism from cultural conservatives.

“We at the Family Research Council oppose including gender identity as a category of protection,” said Peter S. Sprigg, senior fellow for policy studies.

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Mr. Sprigg said his group believed that what it calls “gender identity disorder” should be “treated with therapy to help people be comfortable with their biological sex rather than affirming and celebrating and protecting those who want to deny their biological sex.”

When the administration foreshadowed the change back in June, it was thought the guidelines would be in an updated federal handbook for managers and supervisors. Their inclusion instead in the equal-employment opportunity notices on www.usajobs.gov, the federal jobs site, was viewed as even more significant.