Yemen's southern Abyan province was the scene of a human rights "catastrophe" during fighting between Al-Qaeda-linked militants and government troops, Amnesty International said in a report on Tuesday.
The watchdog spoke of "horrific" rights abuses and called for an impartial government probe into the violations.
"Abyan experienced a human rights catastrophe as Ansar al-Sharia (jihadists) and government forces vied for control of the region during 2011 and the first half of 2012," said Amnesty's regional director Philip Luther.
The watchdog recorded "horrific human rights abuses" in Abyan and other southern areas which fell for around a year under jihadist rule until Yemen's army drove them out in June following an all-out offensive on the region.
The Islamists carried out "public summary killings, crucifixion, amputation and flogging," against residents in these southern areas during their year-long rule, it said.
It blamed Ansar al-Sharia, who are linked to Al-Qaeda in the Arabian Peninsula, for "widespread and disturbing human rights abuses" and said the jihadists set up "religious courts."
These courts "frequently imposed cruel, inhuman and degrading punishments on alleged criminals, suspected spies working against Ansar al-Sharia and people who transgressed cultural norms, including summary killings, amputations and floggings."
Signup to our newsletter and follow us on Facebook and Twitter!
Ansar al-Sharia also "used residential areas as its base, particularly in (Abyan's town of) Jaar, recklessly exposing civilian residents to harm," said Amnesty.
The London-based also accused Yemeni troops of using "inappropriate battlefield weapons such as artillery in civilian residential areas."
"Scores of civilians, including children, were killed and many more injured as a result of air strikes and artillery and mortar attacks by government forces" there during the army offensive, it said.
The army also "appeared to fail to take necessary precautions to spare civilians" in the south, of which an estimated 250,000 people -- most of them from Abyan -- were displaced, it added.
Amnesty said Yemen authorities "must ensure that a commission of inquiry announced in September 2012 covers the truly shocking abuses committed," hold to account those responsible and offer reparations to the victims' families.
The Islamist militants took advantage of the weakness of Yemen's central government during an uprising last year against now ousted president Ali Abdullah Saleh to seize large swathes of territory in the south.
But after a month-long offensive in May launched by Yemeni troops, most militants fled to more lawless desert regions of the east.