In a statement, several civil rights organizations that had submitted a brief opposing the injunction called the ruling unfortunate and premature.

“A ruling by a single judge in one circuit cannot and does not undo the years of clear legal precedent nationwide establishing that transgender students have the right to go to school without being singled out for discrimination,” the groups — Lambda Legal; the American Civil Liberties Union and the A.C.L.U. of Texas; the National Center for Lesbian Rights; the Transgender Law Center; and G.L.B.T.Q. Legal Advocates & Defenders — said in their statement.

The ultimate impact of the Texas decision is unclear and is likely to be limited, legal experts said. For one thing, more senior courts in other regions have agreed with the administration that transgender students and workers are protected by existing laws against sex discrimination, and their decisions will not be altered by the Texas ruling.

Also, the decision will not necessarily affect the outcome of other current cases. In the most prominent one, a federal court in North Carolina is weighing almost identical issues in suits brought by civil rights groups and the Justice Department that seek to block a state law requiring people in government buildings, including public schools, to use bathrooms that correspond to the gender on their birth certificates.

Adding another major note of uncertainty, the United States Supreme Court has temporarily blocked a decision by the Fourth Circuit Court of Appeals that required a school district in Virginia to allow a transgender boy to use the boys’ bathrooms. The Supreme Court issued a temporary injunction until it decides, probably this fall, whether to hear the case.

If the Supreme Court does take the case and reaches a majority decision one way or another, then existing rulings by district and appeals courts could be superseded. If the Supreme Court takes the Virginia case but then is divided, four to four, on the issues, the Fourth Circuit’s existing decision in favor of transgender rights would take effect, although it would not be a nationally binding precedent.

The Texas lawsuit, filed by Mr. Paxton on behalf of officials in 13 states, argued that the Obama administration had overstepped its authority in a series of pronouncements in recent years holding that discrimination against transgender people is a violation of existing laws against sex discrimination, including Title IX in federal education laws and Title VII in federal civil rights laws governing the workplace.