“Ahmed Mohammed Ahmed Haza al-Darbi’s transfer from Guantánamo detention to Saudi Arabia will not take place today,” she said, adding: “We await assurances from the Saudi Arabian government to move forward on his departure. Al-Darbi will remain at Guantánamo until all transfer details are concluded.”

The missed deadline came days after a military commissions judge indefinitely shut down the case against another Saudi detainee — who is accused of orchestrating the 2000 bombing of the American destroyer Cole, and against whom Mr. Darbi testified as part of his cooperation — after more than six years of pretrial hearings.

The fate of Mr. Darbi has been closely watched for several reasons. If the United States lived up to the Obama-era deal, it would mean that President Trump would preside over a reduction of the Guantánamo detainee population, which would drop from 41 to 40, despite his campaign vow to fill it back up.

But if the government reneged on the deal, legal experts have warned that it would strongly discourage other detainees from cooperating with military commissions prosecutors by pleading guilty and potentially serving as witnesses — a key tool that civilian court prosecutors routinely use to win convictions.

Last year, the State Department, under Secretary of State Rex W. Tillerson, dismantled the Office of the Special Envoy for Guantánamo Closure, which had been created by the Obama administration to make diplomatic arrangements for detainee transfers and to handle any subsequent diplomatic issues regarding former detainees. A remaining official was reassigned to help process Freedom of Information Act requests.