A damning report by Amnesty International says that a year after the uprising against Muammar Gaddafi Libya's militias are "largely out of control", with the use of torture ubiquitous and the country's new rulers unable – or unwilling – to prevent abuses.

The report says that the "hundreds of armed militias" that took part in the overthrow of Gaddafi's regime continue to operate more or less independently of the central authorities. Since the fall of Tripoli last August, the militias have failed to disband – and now pose a serious threat to a democratic Libya.

Libya's ruling National Transitional Council (NTC) has "failed to get a grip" on the militia problem, Amnesty says. The NTC has taken no action against fighters from either side involved in human rights abuses, and has not brought to justice those involved in extra-judicial killings – including of Gaddafi and his son Mutassim, captured and executed last October.

Additionally, there is overwhelming evidence that Libya's victorious militias use torture. Thousands of detainees are being held in various prisons across the country. In at least 12 cases since October prisoners have been tortured to death, including Omar Brebesh, Libya's former ambassador to France, who died in Tripoli last month.

Donatella Rovera, author of the Amnesty report, said she witnessed violence against detainees first hand at one militia jail in Misrata. "I was leaving the place, three guys, two in military clothes, were beating the hell out of two detainees," she told the Guardian. "When I said: 'What are you doing?' he [a captor] said: 'These guys are not going to be released.'"

She said she complained, and later returned to the jail, to find the detainees had been freed. But she said Amnesty's call for the NTC to take action had fallen on deaf ears. "I have not seen one single case that is being investigated," she said.

Rovera, who spent several months in Libya, said militia violence against detainees was not universal but that the violence is unchecked: "Within the militias there are members who don't agree with what's going on and feel that they are not able to expose it."

She said Nato nations, who had played a large part in winning the war for the former rebels, should put more pressure on the authorities to act. "Their friends including the UK need to start telling them [The Libyan authorities]. The international friends who supported them, they need to snap out of this self-congratulatory complacent attitude."

Amnesty interviewed dozens of prisoners in January and February. They were being held in and around Tripoli, as well as in the cities of Zawiya, Gharyan, Misrata and Sirte. Detainees said they had been suspended in contorted positions; beaten for hours with whips, sticks and bars; and given electric shocks with live wires and Taser-like weapons. "The patterns of injuries observed were consistent with their testimonies," Amnesty said.

Since the former regime's collapse, the militias have rounded up thousands of suspected Gaddafi loyalists, together with soldiers and alleged foreign mercenaries, the report says. Militias have also looted and burned homes, forcibly displacing tens of thousands of people, and meting out collective punishment against communities seen as having supported Gaddafi during the fighting.

In Misrata, the coastal city that saw some of the worst battles, families who fled have returned to discover that their apartments have been given to other people. Locals have accused them of being traitors and have expropriated or burned down their properties. The Misrata militias have also razed the regime-loyal town of Tawargha, 30km east of Misrata, forcing the entire population of 30,000 to flee.

On a recent visit to Misrata's main military prison, a former school, the Guardian saw no visible signs of mistreatment, with several hundred inmates gathered in the playground area. Approximately 40 prisoners had lined up suitcases and canvas bags, ready to be discharged with prison authorities saying they were no longer suspected of war crimes.

But Médicines Sans Frontières (MSF), which quit treating tortured prisoners last month in protest at continuing torture, said mistreatment occurs at several militia bases elsewhere in Misrata, with the victims returned, wounded, to the former school, and in some cases taken out again for fresh torture. MSF said it has treated 112 detainees who were the victims of torture, some more than once, prompting its decision to quit Misrata in protest.

One none-military source in Misrata said the problem rested with the lack of a command structure for the militias; each prisoner is in effect the property of the militia who arrested him. While some militias may be lenient, others can be harsh, and there is no military police organisation to enforce standards of conduct.

The militias have also detained black Libyans and migrant workers from sub-Saharan Africa – accusing them of being hired Gaddafi mercenaries. Many have been tortured.

"The NTC-led transitional government appears to have neither the authority nor the political will to rein in the militias, many of which are reluctant to submit to the central authority," Amnesty says.

Hana El Gallal, of Libya's National Council for General Freedoms and Rights, a human rights group, said the problem rested with a lack of control over militias. "We do have torture, but it is not systematic, it is individual. We need to address this as fast as possible."

She said a visit to detainees held in a makeshift prison in the coastal town of Sirte in January lasted five minutes, with Amnesty officials told to leave before it was possible to interview and examine the inmates.

"There is a lot the NTC can and should do," she said. "This kind of chaos is very bad for security, for business, for everything in Libya."

Some 2,400 detainees remain in centres controlled by the new Libyan government. But the militias are believed to be holding thousands more. The International Committee of the Red Cross reported that between March and December 2011 it visited 8,500 detainees in some 60 detention centres. Speaking in January, the UN commissioner for human rights, Navi Pillay, said bluntly: "There's torture, extra-judicial executions, rape of both men and women."

Torture was used throughout Gaddafi's brutal 42-year reign. But testimony from detainees suggests that not much has changed. A 29-year-old former soldier told Amnesty he had been visiting Tripoli with a friend last November when two armed men grabbed him and took him to an unknown location. The men, part of a Nafusa mountains militia, accused him of having fought with Gaddafi.

He recalled: "They forced me to lie on my back on a bed and my hands and legs were tied to the frame. In this position I was beaten with fists on my face. Then they beat me with a plastic hose on my feet. Later, I had to turn around face-down and was tied again to the bed. In that position, I was beaten again with a hose on my back and on the head. I was also subjected to electric shocks to various parts of my body including my left arm and chest. The instrument they used was a black stick about 50cm long. My cousin was also subjected to electric shocks."

He continued: "The torture lasted until about 3am. Then they put us in a vehicle and drove us back to the road to Tripoli, where they left us."

Another 45-year-old army officer from Tripoli of Tawargha origin, said he was repeatedly tortured in January after reporting to work at his military base, now occupied by the rebels.

"Even before I was asked the first question I was beaten with a wooden stick and a heavy rubber cable while I was tied with one wrist to the iron bar of a window and with the other to a metal locker or cabinet," he told Amnesty.

"Later they tied me to the metal frame of a bed and beat me again with a rubber cable. The beating caused bleeding injuries and scars are still visible on my body. The beating also dislocated my right shoulder, which needed surgery.

"Two weeks ago my whole body was covered in bruises. They also subjected me to electric shocks through live wires while I was lying on the floor. They put the electricity to different parts of my body – including my wrists and toes. At one point I fainted and they threw water at me to wake me up."

In some cases prisoners died. A postmortem examination into the death of Fakhri al-Hudairi al-Amari - killed last November - found bruise marks in parallel lines across the body; marks of electric shocks; two nails missing on the left hand; burn marks on the forehead, right forearm and left wrist; bruising around both ankles; and severe abrasions on the soles of the feet. Other cases were similar.

Last November Libya's new interior ministry issued a decree prohibiting "revolutionary brigades" from arresting and interrogating suspects. But the decree is widely ignored, Amnesty said.

http://www.guardian.co.uk/world/2012/feb/16/amnesty-widespread-torture-libyan-militias?newsfeed=true