GENEVA (Reuters) - The top U.N. human rights official called on Iraq on Tuesday to stop groups that are fighting alongside government forces against Islamic State from taking revenge on civilians and to clarify the fate of hundreds who went missing.

Witnesses say a government-affiliated Shi'ite militia that helped the army recapture Falluja from Islamic State in early June abducted more than 600 Sunni Muslim men and boys who had just fled the city.

The disappearances, along with one of the worst single bombings in Iraq to date in Baghdad on Saturday "increase the likelihood of a renewed cycle of full-throttle sectarian violence," U.N. High Commissioner for Human Rights Zeid Ra'ad Al Hussein said in a statement.

Islamic State claimed responsibility for the attack late on Saturday in a busy shopping district. At least 175 people were killed.

Zeid said there was a list of 643 missing men and boys, as well as of 49 others believed to have been summarily executed or tortured to death while in the initial custody of Kata'ib Hezbollah, an Iranian-backed Shi'ite militia, after Falluja was re-taken. Tribal leaders believe another 200 are unaccounted for.

"This appears to be the worst – but far from the first – such incident involving unofficial militias fighting alongside Government forces against ISIL"," Zeid said.

He noted that the government was investigating the disappearances and urged it to prevent further incidents and to bring those responsible to justice.

The U.N. has previously called on the Iraqi government to ensure accountability over allegations of abuse. Several military personnel have been arrested."When they asked for water or food or air, they were abused by militia members, told that their treatment was 'revenge for Camp Speicher,' and beaten with shovels, sticks, and pipes," Zeid said, referring to the U.N.-documented killing of 1,700 cadets by Islamic State in June 2014.

Witnesses said at least four men were beheaded, others were handcuffed and beaten to death, and the bodies of at least two men were set on fire, Zeid wrote. People who escape from Islamic State should be treated with sympathy and respect, he said.

"There must be an understanding that most of the male inhabitants of these cities are not willing members of ISIL, nor do they necessarily have anything to do with them at all beyond doing what is necessary to stay alive," he said.

(Reporting by Stephanie Nebehay; Editing by Raissa Kasolowsky)