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"I'm not going to get into identifying potential sites, in part because, frankly, sites that are floated and then shot down have a way of being resurrected," Pentagon press secretary Geoff Morrell told the newspaper.
"So let's let the process continue, and we'll see what the ultimate recommendation is," he said.
President Barack Obama has ordered the closure of the notorious prison at the U.S. naval base in Cuba by Jan. 22, 2010. A military prison at Fort Leavenworth, Kansas has emerged as a likely site to hold the Guantanamo prisoners.
Two Republican senators representing Kansas, however, oppose the arrangement and have put a legislative hold on the nomination of Obama's choice for Army Secretary as a bargaining tool on the issue.
Another possible site for holding the prisoners is the U.S. Marine Corps prison at Camp Pendleton, California.
Obama signed an executive order in January to close the Guantanamo prison within one year but is facing a number of legal and political problems during the process.
The prison was opened in 2002, and currently has 240 detainees.
Recent polls show that most Americans are opposed to closing the prison and transferring its prisoners to U.S. soil.