The UAE, a key U.S. ally, says it has never run prisons or secret detention centers in Yemen.
It and its Yemeni allies have denied past allegations of torturing prisoners.
Amnesty said in a statement on Thursday that scores of men had been subjected to enforced disappearance after being arbitrarily detained by UAE and Yemeni forces “operating outside the command of their own government”.
The UAE is one of the leading countries in an alliance of Arab states fighting in Yemen in support of a government based in the south of the country, against the Houthi movement which controls the capital Sanaa and much of the north.
The UAE mission in Geneva said last month that Yemeni authorities “are in complete control of local and federal governance, judicial and prison systems”.
However, the interior minister in the southern-based regime, Ahmed al-Maysari, appeared to contradict that statement earlier this week by calling on the UAE to shut down or hand over prisons it runs.
On Tuesday, Maysari said he had reached an agreement with the UAE and that now all prisons in the government-held areas are under the control of the Yemeni general prosecutor.
Amnesty said an investigation conducted between March 2016 and May 2018 in the southern provinces of Aden, Lahj, Abyan, Shabwa, and Hadramout documented widespread use of torture and other ill-treatment in Yemeni and Emirati facilities, including beatings, use of electric shocks and sexual violence.
“The UAE, operating in shadowy conditions in southern Yemen, appears to have created a parallel security structure outside the law, where egregious violations continue to go unchecked,” said Tirana Hassan, Crisis Response Director at Amnesty International.
“Ultimately these violations, which are taking place in the context of Yemen’s armed conflict, should be investigated as war crimes,” Hassan said.
The Amnesty report also called on the United States to do more to ensure it does not receive information obtained by its UAE allies through torture, and to promote compliance with human rights laws.