WASHINGTON — In an extraordinary Supreme Court filing on Friday, the Justice Department accused the American Civil Liberties Union of misconduct in the case of an undocumented teenager in government custody known as Jane Doe. The teenager obtained an abortion last month over the government’s objection after an appeals court allowed it.

“The A.C.L.U. misled the United States as to the timing of Jane Doe’s abortion,” said Devin M. O’Malley, a Justice Department spokesman. “After informing Justice Department attorneys that the procedure would occur on October 26th, Jane Doe’s attorneys scheduled the abortion for the early morning hours of October 25th, thereby thwarting Supreme Court review. In light of that, the Justice Department believes the judgment under review should be vacated, and discipline may be warranted against Jane Doe’s attorneys.”

David Cole, the A.C.L.U.’s legal director, said the accusations were baseless.

“The Trump administration blocked Jane Doe from getting constitutionally protected care for a month and subjected her to illegal obstruction, coercion and shaming as she waited,” he said. “After the courts cleared the way for her to get her abortion, it was the A.C.L.U.’s job as her lawyers to see that she wasn’t delayed any further — not to give the government another chance to stand in her way.”

“This administration has gone to astounding lengths to block this young woman from getting an abortion,” Mr. Cole said. “Now, because they were unable to stop her, they are raising baseless questions about our conduct. Our lawyers acted in the best interest of our client and in full compliance with the court orders and federal and Texas law. That government lawyers failed to seek judicial review quickly enough is their fault, not ours.”