"The Emirati state, a member of the Arab coalition, does not administer or supervise any prison in Yemen," the foreign ministry said in a statement.
The UAE is a key member of a Saudi-led military coalition that entered Yemen's conflict in 2015 to battle on the government's side against Iran-backed Huthi rebels.
Human Rights Watch said on Thursday that the UAE runs at least two "informal detention facilities" in Yemen and has reportedly transferred detainees to a base in Eritrea.
The New York-based group said the UAE also runs detention facilities in southern provinces home to Al-Qaeda in the Arabian Peninsula and a local affiliate of the Islamic State group.
The foreign ministry rejected the allegations as "totally unfounded", saying UAE forces "respect international conventions on armed conflicts".
The World Health Organisation estimates more than 8,000 people have been killed in two years of conflict in Yemen.