DUBAI (Reuters) - Amnesty International accused the United Arab Emirates (UAE) and allied Yemeni forces of torturing detainees at a network of secret prisons in southern Yemen and said such violations should be investigated as war crimes.

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”, Amnesty said in a statement.

The UAE, a key U.S. ally, says it has never run prisons or secret detention centers in Yemen and that prisons there are under the authority of the Yemeni government. It and its Yemeni allies have denied past allegations of torturing prisoners.

“The UAE has urged the Yemeni government to conduct an independent investigation into the matter and continues to follow up with the Yemeni government on this front”, UAE authorities said in a statement responding to the report.

“The UAE believes that these reports are politically motivated to undermine its efforts as part of the Arab coalition to support the Yemeni 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 Iran-aligned 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 government, 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.”

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.