Yemen's interior minister has demanded the United Arab Emirates shut down or hand over secret prisons that The Associated Press reported are under the control of the UAE and its allied militias.

At least 80 detainees have been freed from the facilities in recent weeks since an AP investigation detailed sexual abuse and torture at the sites.

It was the first time Interior Minister Ahmed al-Maysari has gone public with the demand in talks with an Emirati official, seeming to contradict the UAE's repeated denials that it has authority over any prisons in Yemen.

The AP first reported in an investigation last year that the UAE and its allied militias were running a network of secret detention facilities around southern Yemen, beyond the control of Yemeni President Abed Rabbo Mansour Hadi's government.

Former prisoners and security officials described widespread torture at the facilities, which are housed in locations ranging from Emirati-run military bases to a former nightclub run by a UAE-backed security chief and his anti-terrorism squad.

A deserted cell in the public section of Aden Central Prison is shown in this May 9, 2017 photo in Aden, Yemen (AAP)

Thousands of Yemenis swept up in the US-backed campaign against al-Qaida have been held in the prisons without charges or trials. Some have been interrogated by U.S. personnel inside the facilities, the AP found.

In June, the AP revealed that hundreds had been subjected to sexual abuse, including one incident in the Beir Ahmed prison in the southern city of Aden, where detainees were lined up naked as guards probed their anal cavities. Sexual abuses were filmed as a way to turn suspects into informants, detainees reported.

On Sunday, Anwar Gargash, the UAE state minister for foreign affairs, dismissed as "fake news" reports that his country controls prisons or has set up a base on the Yemeni island of Socotra.

"In Yemen, the Emiratis have been subjected to an unjust smear campaign because it bears its responsibility toward regional security with courage and boldness," he said.

In Yemen's three-year civil war, the UAE is part of the Saudi-led coalition battling Iranian-backed rebels known as Houthis who have taken over most of northern Yemen.

View through a mesh window over part of Aden Central Prison, known as Mansoura, in Aden, Yemen. (AAP)

Ostensibly, the Emiratis and Hadi's government are allies in that fight. But tensions have been high between them.

The UAE has built up militias across southern Yemen that government officials say are only loyal only to the Emiratis.