The London-based human rights group said 500 detainees continued to be held without charge or trial and repeated its call for the centre to be shut.
Meanwhile, cases against a Canadian and a Yemeni detainee are getting under way at tribunals at the centre in Cuba.
Such tribunals are also criticised for failing to give suspects a fair trial.
Amnesty said there were mounting allegations of appalling conditions, torture and ill-treatment of detainees at Guantanamo Bay.
'No middle ground'
The group highlighted the case of Jumah al-Dossari - a 32-year-old Bahraini who was taken to Guantanamo Bay in January 2002.
His lawyer said Mr Dossari had been urinated on, threatened with rape and had his head repeatedly smashed against the floor. The claims have been denied by the US government.
He had reportedly attempted to commit suicide 10 times, the rights group said.
Another detainee, Sami al-Hajj - a Sudanese cameraman for Arab satellite TV network al-Jazeera - had been subjected to severe physical, sexual and religious abuse over the last four years, his British lawyer Clive Stafford-Smith said.
Amnesty's UK Campaigns Director, Stephen Bowen, called the situation at Guantanamo Bay "shocking".
"There's no middle ground regarding Guantanamo. It must be closed and there must be an investigation into the dozens of torture reports that have emerged since 2002," he said.
Supreme Court ruling
On Wednesday, Ali Hamza al-Bahlul, a Yemeni accused of being Osama Bin Laden's bodyguard, was appearing before a military tribunal for a pre-trial hearing.
He has asked to defend himself against a charge of conspiracy to commit war crimes.
A pre-trial hearing is also being held for 19-year-old Canadian detainee Omar Khadr, who is accused of killing a US army medic in a firefight at a suspect al-Qaeda base in Afghanistan.
If convicted, the two men could face life in prison.
The cases have gone ahead even though the trials of other Guantanamo detainees have been halted while the US Supreme Court decides if US President George W Bush had the authority to establish such tribunals.
The Bush administration argues that it needs flexibility in dealing with the war on terror and terrorists cannot be treated as if they are just another criminal defendant.
Sen. Carl M. Levin (D-Mich.) said yesterday that the Bush administration cannot use recent legislation he helped craft to seek the dismissal of habeas corpus petitions filed on behalf of detainees at Guantanamo Bay, Cuba, contending that the law applies only to new cases. Justice Department lawyers filed notice in federal courts in Washington this week that the administration will attempt to have 186 pending cases dismissed beginning Monday. They plan to use the newly signed law to argue that the court no longer has jurisdiction to hear the prisoners' cases. The administration also wrote a letter to the U.S. Court of Appeals for the District of Columbia Circuit indicating that lawyers plan to file a motion next week "to govern further proceedings in these cases in light of the new legislation." The new language, which President Bush signed into law Friday, restricts Guantanamo Bay prisoners' federal court filings to one review of their status as enemy combatants. It also allows detainees convicted in military trials to appeal those convictions. In a 2004 Supreme Court decision, the prisoners won the right to file habeas corpus petitions contesting their incarcerations. But Levin and Sen. Lindsey O. Graham (R-S.C.) wanted to limit further access to the courts via those petitions. In an interview yesterday, Graham disagreed with Levin, saying that he believes the legislation does not preserve existing lawsuits. "The courts will decide whether to proceed in pending cases," Graham said. Levin, however, said he rebuffed at least three administration efforts to make the law retroactive while the legislation was being written. He specifically objected each time, and a compromise bill ultimately was written so that it would apply only to future cases, according to a written statement from his office yesterday. Legal experts said yesterday that the administration may have room to interpret the law because its language is somewhat vague. It says that the law would "take effect on the date of the enactment" and does not address whether the law applies to pending cases. The Center for Constitutional Rights, which represents hundreds of detainees at Guantanamo Bay, filed additional habeas corpus petitions late last week in an attempt to give more detainees access to the courts before the law took effect, said Bill Goodman, the center's legal director. Goodman said nearly all of the approximately 500 prisoners in Guantanamo Bay now have cases pending in federal courts. The Bush administration interpreted the new law as applying to all detainee cases, pending or not yet filed, according to a White House signing statement on Friday. Justice Department lawyers believe the law removes the court's jurisdiction, preventing judges from hearing such cases. Citing the access to courts still provided by the new law, Tasia Scolinos, a Justice Department spokeswoman, said yesterday that "we are aware of no other country that has provided their enemies with such extensive legal review during an ongoing conflict." District Judge Reggie B. Walton, who is presiding over several detainee cases, moved swiftly yesterday, issuing orders asking lawyers for the detainees to show in court why their cases "should not be dismissed for lack of jurisdiction." The orders require detainees' attorneys to make such arguments by Jan. 12. "The Act raises serious questions concerning whether this court retains jurisdiction to hear this case and all related matters," Walton wrote in an order released yesterday. Michael C. Dorf, a law professor at Columbia University, said he was not surprised the administration moved quickly to try to have the cases dismissed. "I think the administration has a plausible argument that it applies to pending cases," he said. "It is legitimately ambiguous language. This is a gift from Congress, enabling them to remove jurisdiction. Why wouldn't they do it right away? In a way, I'm surprised they waited three days." But Madeline Morris, a law professor at Duke University and adviser to the chief defense counsel for the military commissions at Guantanamo Bay, said yesterday that she believes the law's language clearly does not apply to previously filed cases. She said the administration is seeking "to reduce and limit the scope of judicial oversight and involvement in these cases," but that the courts, ultimately, will have the final say unless Congress again steps in. Levin said in his statement that "the administration is now seeking to end-run the legislative process and achieve a result through the courts that it was unable to obtain in Congress. I hope and expect that the courts will reject this effort." Staff writer Carol D. Leonnig and researcher Julie Tate contributed to this report.