The decision has been taken without prior consultation with the Iraqi civil society or the international community, Amnesty said in a statement issued on Thursday.
It also questioned the US-led authority, as an occupying power, to establish such a tribunal under international humanitarian law.
"We have been urging that the proposals to establish the tribunal be subject to widespread consultation within Iraq civil society, especially the legal profession and human rights
groups, as well as the international community," Amnesty International said.
"Unfortunately, the draft statute of the tribunal was not made public before its adoption."
Amnesty also said it was concerned about reports that the tribunal would "use Iraqi criminal code, some aspects of which are inconsistent with international human rights standards, to
regulate trial procedures and define crimes and punishments."
"We are particularly concerned that the Iraqi Penal Code provides for the death penalty for crimes under the jurisdiction of the tribunal," it said.
"We have been urging that the proposals to establish the tribunal be subject to widespread consultation within Iraq civil society, especially the legal profession and human rights groups, as well as the international community"
The president of Iraq's Governing Council said on Thursday the United States would hand over key members of the former Iraqi regime to the special tribunal and Saddam Hussein could face trial in absentia.
"We agreed that those who have been accused and detained would be handed over to this historic court," Abd al-Aziz al-Hakim told a news conference.
He called the creation of a tribunal to try crimes against humanity and genocide a "great achievement for the Governing Council in Iraq".
Hakim said Iraqis who had committed crimes against humanity during the 1980-1988 war with Iran and the 1990 invasion of Kuwait could also face the tribunal.
Saddam to be charged
Ahmad Chalabi, a senior member of the US-backed Governing Council, said: "Saddam Hussein will be accused and charged with committing crimes against humanity and the Iraqi people.
He will certainly come under the jurisdiction of this court."
The death penalty, which was often used under Saddam's rule, has been suspended under US-occupied Iraq. But Chalabi
suggested it could still be applied against Saddam and his closest aides if they were convicted.
"There is a provision for imposing the death penalty in the
body of the law," he said.
Washington hopes prosecuting Saddam's top lieutenants will
help bolster support for the Governing Council and convince Iraqis the old regime will not return.