“Chelsea is a tremendously courageous person and this outcome was not unexpected but this an appealable order,” said her lawyer, Moira Meltzer-Cohen, after the hearing.

Joshua Stueve, a spokesman for the United States attorney in the Eastern District of Virginia, said the government did not want to confine Ms. Manning, relaying a statement that Tracy Doherty-McCormick, a federal prosecutor, had made after the judge opened part of the contempt hearing on Friday.

“It has always been our intent and hope for her to testify and comply with the valid court order and valid grand jury investigation,” Ms. Doherty-McCormick said. “Ms. Manning could change her mind right now and do so. It is her choice. This is a rule of law issue, and Ms. Manning is not above the law

In a lengthy confession in 2013, Ms. Manning said she had interacted online with someone who was likely Mr. Assange. But she said she acted of her own accord and was not directed by anyone at WikiLeaks. Ms. Manning said prosecutors had wanted her to go over those same events.

“The grand jury’s questions pertained to disclosures from nine years ago, and took place six years after an in-depth computer forensics case, in which I testified for almost a full day about these events,” she said in the statement. “I stand by my previous testimony. I will not participate in a secret process that I morally object to, particularly one that has been historically used to entrap and persecute activists for protected political speech.”

A military judge in 2013 had sentenced Ms. Manning to 35 years in prison, and, and counting her time in pretrial custody, she served about seven years — by far the longest prison time any American has served for leaking government secrets to the public — before President Barack Obama commuted the remainder of her sentence in 2017. As a transgender person struggling to transition to life as a woman, she had a difficult time in a male military prison and twice tried to commit suicide in 2016.

The contempt hearing on Friday was partly closed, but the judge had opened it for a portion in which Ms. Meltzer-Cohen argued that Ms. Manning should be confined at home. The judge rejected that request and Ms. Manning was taken to the women’s wing of the federal detention center in Alexandria, Va., Ms. Meltzer-Cohen said.

Mr. Stueve said federal officials had taken steps to ensure that Ms. Manning’s medical needs would be met while she remained in custody.

Confinement for defying a grand-jury subpoena can last until the term of the jury is over, after which prosecutors would have to obtain a new subpoena and start the process over if they wanted to continue to press the issue. Both Ms. Meltzer-Cohen and Mr. Stueve declined to say when the current jury’s term is set to end.