The men were captured in Afghanistan where they said they were sheltering from repression from Chinese authorities in their home region of Xinjiang.
The US government has said it no longer considers the men enemy combatants and has given no evidence that they pose a security risk.
It is thought to be trying to find new homes for the men in third countries, having apparently accepted their claims that they face torture or possible execution if they are returned to China.
China has said it considers the men to be terrorists.
Albania agreed to accept five Uighur detainees in 2006 but has refused to take more, partly because of fears of a diplomatic backlash from offending China.
The two judges who voted to block the Uighurs' immediate release were both appointees of the first President Bush, while Judge Judith W. Rogers, who was appointed by President Clinton, argued that the detainees should be freed.
In a stern four page statement she noted that the Bush administration continued to argue the detainees were a national security risk based on little more than the fact they had admitted to receiving weapons training in Afghanistan.
"The fact that petitioners received firearms training cannot alone show they are dangerous, unless millions of United States resident citizens who have received firearms training are to be deemed dangerous as well," Rogers wrote.
"And, in any event, the district court found there is no evidence petitioners harbour hostility toward the United States."