President Bush has dug in his heels on the issue of whether to close the war prison at the U.S. military base on Cuba’s Guantanamo Bay.

His decision runs against the advice of his new defense secretary, Robert M. Gates, his secretary of state, Condoleezza Rice, many members of Congress, and many allied nations.

But the backing of Vice President Dick Cheney and Attorney General Alberto R. Gonzales evidently has persuaded Mr. Bush to go against much domestic and world opinion and even his own stated preference for closing the base. A newly reconstituted military trial system on Guantanamo took up its first case this week and obtained a conviction.

The dispute over Guantanamo’s future broke into the open with a New York Times report on March 23 that Mr. Gates started his new job with repeated recommendations that Guantanamo had become so tainted abroad that no trials there would be considered legitimate. The Times reported that he told Mr. Bush that the detention facility should be closed down as quickly as possible but that counterarguments by Mr. Cheney and Mr. Gonzales and some other government lawyers had prevailed. They raised strong objections to moving detainees to the United States.

It was not the first outbreak of an administration split on the issue. In 2005, Time magazine had reported in detail the torture at the base of the reported 20th hijacker, Mohammad al-Kahtani, with dogs, injections and sexual humiliation. Mr. Bush reacted by saying repeatedly that he wanted Guantanamo closed and was “exploring all alternatives.” But Mr. Cheney disagreed publicly, declaring in a Fox TV interview: “The important thing here to understand is that the people that are at Guantanamo are bad people.”

Some are and some perhaps aren’t. A recent Amnesty International analysis of 500 detainees found that only 25 of them had been captured by U.S. forces. Another 430 of them had been arrested by Pakistani forces or by the Afghan Northern Alliance when handing over a “terrorist” would bring a reward of up to $5,000.

The problem was that there has been no effective way to tell the real, confirmed terrorists from the poor bystanders who had been caught up in dragnets and lumped together in Mr. Cheney’s collection of “bad people.” They still can’t use habeas corpus, and only a few Republicans have joined the Democrats to restore it.

Does Mr. Bush’s insistence mean that the Guantanamo prison will keep operating as long as he remains president? Don’t bank on it. The two officials who urged his decision are both losing influence. The betting in Washington is that Mr. Gonzales will soon be out of office. And Mr. Cheney, who ran an influential independent national security operation out of the vice president’s office for six years, has lost his chief allies in the Pentagon and the State Department.

President Bush may yet see that Guantanamo is a national shame and close it down.