Bush on Wednesday said the prison should be closed down, but said a plan for relocating the prisoners was needed first and he also was awaiting a Supreme Court decision about the forum for handling detainee cases.
"I'd like to close Guantanamo, but I also recognise that we're holding some people there that are darn dangerous and that we better have a plan to deal with them in our courts," Bush told a news conference in the White House Rose Garden.
The number of detainees may be reduced by nearly a fifth, according to an Afghan official who said there were plans to extradite all 96 Afghans, including several senior Taliban officials.
The US military declined to confirm or deny the information, citing security concerns about discussing any movements of prisoners before they take place.
Bush said Guantanamo was seen by some countries as an example of the United States not living up to the principles it espouses on human rights.
"No question, Guantanamo sends, you know, a signal to some of our friends - provides an excuse, for example, to say, 'The United States is not upholding the values that they're trying encourage other countries to adhere to,'" Bush said.
About 460 people are being held
in the Guantanamo prison
The US military is holding 460 foreigners at the Guantanamo prison, many of whom were captured in Afghanistan in the US-led war to topple the Taliban and al-Qaeda after the September 11 attacks. Nearly all are being held without charge.
Two Saudis and a Yemeni were found dead at the prison on Saturday after hanging themselves with clothes and bedsheets.
The suicides were the first prisoner deaths at Guantanamo, although there have been many previous suicide attempts and hunger strikes since the United States began sending suspected al-Qaeda and Taliban captives there in 2002.
Guantanamo is one of several issues that have undermined support abroad for Washington's war on terrorism, declared after the September 11 attacks.
The suicides came amid an investigation of US Marines after an alleged massacre of two dozen civilians at Haditha, Iraq, in November 2005 and after the Abu Ghraib prison abuse scandal.
Bush, who spoke hours after returning from a surprise visit to Iraq, said he was asked about such cases by a member of the Iraqi cabinet. He promised to deal with the incidents.
"I also want the people to understand, here and around the world, that 99.9% of our troops are honourable, decent people who are serving our country under difficult conditions," Bush said.
The US Supreme Court is expected to rule this month on the legitimacy of special military tribunals set up to try some of the Guantanamo prisoners for war crimes. Ten detainees face hearings before the tribunals.
Bush said the United States was also in a difficult position in some cases in which it wanted to send prisoners back to their countries.
Some of the measures have been criticised because of concerns the prisoners may face torture by their home countries.