The human rights group also blamed the US-led and Iraqi security forces for "grave human rights violations", with thousands being held without charge or trial in US detention centres in Iraq and reports of systematic torture by Iraqi forces.
"Torture and ill-treatment were reported in secret detention centres, police stations and official detention centres," the group said in its annual report published on Tuesday.
Amnesty said About 14,000 people - most of them Sunnis arrested in fighter strongholds - were being held as of November 2005 in four US-run facilities in Iraq, including Abu Ghraib prison.
It also said covert detention facilities and harsh emergency laws in several other Arab countries paved the way for a wider net of arbitrary arrests, incommunicado detention and torture of terrorist suspects as well as political dissidents.
"There was increasing information to indicate that individuals suspected of terrorism by the US authorities have been secretly and forcibly transferred to others countries, including Egypt, Morocco, Jordan and Syria, for interrogation," it said.
"Torture and ill-treatment were reported in secret detention centres, police stations and official detention centres [in Iraq]"
The group said most transfers were made to countries "whose security services had long records of torturing detainees with impunity".
It added that Britain had signed agreements with Lebanon, Libya and Jordan, noting a "further sign of close collaboration ... under which they agreed to accept individuals whom the UK authorities wished forcibly to expel".
Even though the three countries signed memorandums promising not to torture inmates, Amnesty described the move as "implicit recognition that these countries had failed to respect the guarantees against torture to which they had previously committed under international law".
According to Amnesty, scores of people were being held in secret detention facilities at the behest of the US, in Jordan and Egypt although the authorities have denied this.
In particular, a number of defendants tried in Jordan's state security courts said "they had been tortured to extract confessions".
Fresh reports of torture also emerged in Egypt, whose prime minister reported in May that "more than 60 people had been forcibly transferred to Egypt by US forces" since the September 11, 2001 attacks on the US.
Amnesty says thousands are
being held without charge in Iraq
The report also said that about 200 people in Yemen "continue to be detained without charge or trial as suspects in the 'war on terror'".
Amnesty "interviewed detainees in Yemen who said they had been briefly detained and tortured in Jordan and then held for many months in secret detention centres under US control, whose location they never learned".
In addition to alleged terrorist suspects, political dissidents landed in jail at alarming rates in Syria, Iran and Egypt, while Lebanon saw a spate of apparently targeted killings against opposition politicians and journalists.
In Libya and Tunisia, "many political prisoners, including prisoners of conscience were believed to be held and several new arrests were reported".
It alleged that human rights abuses were inflicted in Morocco "in the context of the war on terror", with thousands of suspected Islamist activists arrested following deadly bomb attacks in Casablanca in 2003.
The report also attacked widespread censorship and restrictions on freedom of expression and association, including the jailing of journalists, in these countries.
And it complained of impunity for abusers, saying that wrongdoers are escaping justice in countries where steps are being taken to resolve internal conflicts.
The report also expressed concern at evidence that slavery was still being practised in the northwest African state of Mauritania.