In television appearances Sunday, Air Force Gen. Richard Myers, chairman of the Joint Chiefs of Staff also said US officials believe al-Qaida leader Abu Musab al-Zarqawi is wounded, but it's not known how badly.
Muslims in several countries have demonstrated in recent weeks over allegations that a Quran, their faith's holy book, was flushed down a toilet by guards at Guantanamo. Myers denied that.
Quran was mishandled 5 times: Probe
The human rights group Amnesty International also released a report last week calling the prison camp "the gulag of our time."
Myers said the report was "absolutely irresponsible." He said the United States was doing its best to detain fighters who, if released, "would turn right around and try to slit our throats, slit our children's throats."
"This is a different kind of struggle, a different kind of war," Myers said
"We struggle with how to handle them (the prisoners), but we've always handled them humanely and with the dignity that they should be accorded."
Myers repeated the Pentagon's contention that five cases of mistreatment of the Quran at Guantanamo had been confirmed. He did not give any other details about the mistreatment.
The US military had detained more than 68,000 people since the terrorist attacks of Sept. 11, 2001, he said, and looked into 325 complaints of mistreatment. Investigations have found 100 cases of prisoner mistreatment and 100 people have been punished, the general said.
On Zarqawi, who heads the al-Qaida insurgency in Iraq, Myers said US officials believe postings on a militant Web site that Zarqawi had been wounded in a battle. He said he did not know whether Zarqawi had left Iraq for treatment in another country, as some Web sites and news organizations have reported.
In London, The Sunday Times reported that Zarqawi was being treated in Iran after a piece of shrapnel hit his chest during an attack on his convoy. Iran denies it is harboring Zarqawi.