The agencies were asked to consider three potential versions of the order and make recommendations by this week, according to an official familiar with that process.

One was the version that Mr. Trump was preparing to sign three weeks ago. It would reverse a January 2009 order by President Barack Obama that directed the government to close the prison, and make clear that the Trump administration’s policy was instead to keep it open indefinitely, the official said.

That version would also say that Guantánamo could be used to hold accused members of Al Qaeda or the Islamic State, the official said. Transferring Islamic State suspects there would defy warnings by national security and legal officials about creating legal risks for the broader military campaign underway in Iraq and Syria.