In an order issued late Thursday, U.S. District Judge Gladys Kessler said the physical condition of Syrian prisoner Abu Wa'el Dhiab was rapidly deteriorating and she would not reissue a temporary order from last week that stopped the military from force-feeding him.
Dhiab's lawyers have argued that the practice of forcibly extracting him and other prisoners from their cells, restraining them and feeding them through a tube inserted into their noses, was illegal and abusive.
Earlier this week, Kessler said she urged the government and Dhiab's lawyers to reach a compromise on the procedure used to feed Dhiab, but that the Defense Department has "refused to make these compromises."
In a harshly worded, three-page order, Kessler said she faced a "Hobson's choice" of either reissuing a halt to the practices, which risked Dhiab dying, or allow medical personnel to take action to keep him alive at the possible cost of "great pain and suffering."
Lieutenant Colonel Todd Breasseale, a Pentagon spokesman, said: "As the court has asserted, this is a deeply complex issue. The Department has long held that we shall not allow the detainees in our charge to commit suicide and it's particularly worth noting here that we only apply enteral feeding in order to preserve life."
Enteral feeding refers to the delivery of a nutritionally complete food directly into the stomach or small bowel of a person suffering from or at risk of malnutrition.
Prisoners at the Guantanamo Bay naval base have engaged in hunger strikes for years, but only won the right to challenge in U.S. courts the military's practices of forcing them to eat in February.
Dhiab's lawyers are ultimately seeking an order that would force the military to change the practices.
On Wednesday, Kessler ordered the government to turn over more than 30 videos of Dhiab's feedings, some of his 2013 medical records, and the protocols the military uses to force-feed prisoners.