An Amnesty International report has painted a terrifying picture of life in southern Yemen, with militants carrying out arbitrary amputations, floggings, summary executions and even a public crucifixion in a town square.

The Abyan province was controlled by an Al Qaeda-linked militia called Ansar al-Sharia for more than a year, before the militants were driven out by government troops with US backing in June.

In a report entitled Conflict in Yemen: Abyan's Darkest Hour, Amnesty accused Ansar al-Sharia and the Yemeni government of "gross and deeply disturbing abuses".

"Abyan experienced a human rights catastrophe as Ansar al-Sharia and government forces vied for control of the region during 2011 and the first half of 2012," said Philip Luther, Amnesty's director for the Middle East and North Africa.

"The tragedy of Abyan will haunt Yemen for decades to come unless those responsible are held to account, and victims and their families receive reparations."

Amnesty also accused Yemeni government forces of using excessive force in its fight against Al Qaeda.

"Yemeni government forces used inappropriate battlefield weapons such as artillery in civilian residential areas, and in other attacks failed to take necessary precautions to spare civilians," the Amnesty report said.

Amnesty said it had documents showing that "religious courts" set up by Ansar al-Sharia had frequently imposed cruel, inhuman and degrading punishments on alleged criminals and suspected spies working against it in the city of Jaar.

One of the alleged criminals, named as Saleh Ahmed Saleh al-Jamli, 28, was killed and his remains crucified after a court in Jaar found him guilty of planting electronic devices in two vehicles carrying Ansar al-Sharia commanders.

The rights group also said that the militants also conducted public summary executions, amputation and flogging during their rule of Jaar.

The human rights group called for "an immediate and impartial investigation" into the violations.

A spokesman for the Yemeni embassy in Washington, Mohammed al-Basha, said in a statement: "The Yemeni government will carefully examine the findings of Amnesty International's most recent report."

Rights group said the fighting led to the displacement of nearly 250,000 from the southern provinces which were affected by the conflict.

Despite being routed from southern strongholds, Al Qaeda in the Arabian Peninsula (AQAP) continues to pose a major threat to Yemen.

The group has carried out a number of suicide bombings since June targeting military and security facilities and senior officials.

ABC/wires