"I'd like to see it shut down," Admiral Mike Mullen said. "I believe that from the standpoint of how it reflects on us that it's been pretty damaging."
But Mullen, the chairman of the US military's Joint Chiefs of Staff, said closing the prison posed major legal problems.
"There are enormous challenges associated with that," he said. "There are enormously complex, complicating legal issues that are way out of my purview."
McConnell's comments on waterboarding come as the US House Intelligence Committee continues an investigation into the CIA's destruction of videotapes that are reported to have shown the use of the interrogation technique on suspects.
He also said that should waterboarding ever be determined as torture, "there will be a huge penalty to be paid for anyone engaging in it".
"If I had water draining into my nose, oh God, I just can't imagine how painful!" he said.
"We think it's vitally important he and the intelligence community have all the tools they need"
White House spokesman
"Waterboarding", involves pouring water over subjects who are bound, gagged and hooded in order to terrify them by stimulating the feeling that they are drowning.
McConnell stopped short of categorically describing the interrogation process as torture and declined to say whether he believed it should be formally labelled as such.
A spokesman for McConnell later said the intelligence director did not dispute the quotes attributed to him in the story the Associated Press reported.
Kevin Lanigan, from Human Rights First, told Al Jazeera: "It's a very important step for such a senior official in this [US] administration for the first time to admit that - with some caveats on his admission - that this technique is torture."
Michael Mukasey, the US attorney general, has declined to rule on whether "waterboarding" is torture.
A ruling that the technique does constitute torture would put at risk the CIA interrogators who were given permission by the White House in 2002 to use the technique on three prisoners who were considered resistant to conventional interrogation.
McConnell said in his interview that the legal test for torture should be "pretty simple", suggesting: "Is it excruciatingly painful to the point of forcing someone to say something because of the pain?"
The CIA has said it has not used the technique since 2003 and Michael Hayden, the agency's director, prohibited it in 2005.
Tony Fratto, a White House spokesman, refused to comment on the issue on Saturday.
He said: "We don't talk about interrogation techniques. And we are not going to respond to every little thing that shows up in the press.
"We think it's vitally important he and the intelligence community have all the tools they need."
The House and Senate intelligence committees want to prohibit the CIA from using any interrogation techniques not allowed by the military, including so-called waterboarding.
If their bill authorising intelligence activities for 2008 is approved by Congress, it will almost certainly face a veto from George Bush, the US president.
Last summer he issued an executive order allowing the CIA to use "enhanced interrogation techniques" that go beyond what is allowed in the 2006 Army Field Manual.
The House of Representatives has approved the bill, but the Senate is yet to vote on it because of objections to the restrictions it imposes.