BOSTON — A federal judge wants to know why a doctor from Lebanon with a U.S. visa was deported after he ordered that she not be removed until he could hear her case.

Dr. Rasha Alawieh, 34, had been granted the visa Tuesday and arrived at Boston Logan International Airport on Thursday, according to a complaint filed on her behalf by a cousin in federal court.

Alawieh, who had worked and lived in Rhode Island previously, was detained at least 36 hours, through Friday, and was going to be sent back to Lebanon, the complaint said. Alawieh, a kidney transplant specialist, was to start work at Brown University as an assistant professor of medicine.

U.S. District Judge Leo Sorokin issued an order Friday that an in-person hearing be scheduled Monday, with Alawieh brought to court.

“Whether or not she is in custody of the United States, the court anticipates proceeding with this hearing,” he wrote.

But by Saturday, the cousin filed a motion that customs officials “willfully” disobeyed the order by sending Alawieh back to Lebanon.

Sorokin gave the government until Monday morning to respond, before the start of the scheduled 10 a.m. hearing. The government’s response was not publicly available.

Alawieh had worked at Brown before the issuance of her H1B visa, the complaint said. It said she has held fellowships and residencies at three universities in the United States.

A spokesperson for Brown said Alawieh is an employee of Brown Medicine with a clinical appointment to Brown.

Brown Medicine is a not-for-profit medical practice that is its own organization and serves its own patients directly. It is affiliated with Brown University’s medical school.