It said its delegates met detainees held in Tripoli, in Misrata and in smaller towns such as Ghariyan who showed visible signs of torture inflicted in recent days and weeks.
"The torture is being carried out by officially recognised military and security entities, as well by a multitude of armed militias operating outside any legal framework," it said.
Donatella Rouvera, senior adviser at Amnesty, said in the statement that it was "horrifying to find that there has been no progress to stop the use of torture".
"We are not aware of any proper investigations into cases of torture," she said.
Detainees told Amnesty they had been beaten for hours with whips, cables, plastic hoses, metal chains, bars, wooden sticks and given electric shocks with live wires.
The watchdog said the detainees, both Libyans and foreigners from sub-Saharan Africa, were tortured soon after they were seized by militias in officially recognised detention centres in places like Misrata.
Misrata withstood a devastating siege by Kadhafi's forces during last year's uprising. Its fighters later unleashed a fierce attack on the dictator's hometown of Sirte, where he was killed on October 20.
"Several detainees have died in the custody of armed militias in and around Tripoli and Misrata in circumstances that suggest torture," Amnesty added.
Rouvera said the issue was aggravated as the police and judiciary remained "dysfunctional" cross Libya.
Libyan Justice Minister Ali H'mida Ashur neither confirmed nor denied the allegations, but told AFP that "when such complaints reach the general prosecutor or the military prosecutor, necessary action will be taken."
He said the authorities have set up a committee to monitor jails across the country and acknowledged that some prisons were under the control of militias.
Doctors Without Borders said it has suspended its work in Misrata where detainees are "being tortured and denied urgent medical care."
It said its doctors were increasingly confronted with patients who suffered injuries caused by "torture" during questioning.
"The interrogations were held outside the detention centres," it said.
Its general director Christopher Stokes said some officials have sought to exploit and obstruct its work in Misrata.
"Patients were brought to us in the middle of interrogation for medical care, in order to make them fit for further interrogation. This is unacceptable," he said.
"Our role is to provide medical care to war casualties and sick detainees, not to repeatedly treat the same patients between torture sessions."
On Wednesday, the UN special representative in Libya, Ian Martin, expressed concern about the militias which he said were not under the control of the interim government.
Speaking to the UN Security Council, Martin said fighting in the Libyan town of Bani Walid this week -- at one stage blamed on Kadhafi loyalists -- had been caused by a clash between local people and a revolutionary brigade unit.
"Although authorities have successfully contained these and other more minor incidents that continue to take place across the country on a regular basis, there is the ever present possibility that similar outbreaks of violence could escalate," he said.
Libya's new authorities are struggling to integrate tens of thousands of militiamen into the army and police.