The UAE is one of the Arab countries fighting formally on behalf of Yemen's internationally recognized government against the Iran-aligned Houthi movement that controls the capital.
But the UAE has had a tense relationship with the government and has recruited thousands of fighters from a movement of southern separatists who have clashed with government troops.
Yemeni officials said around 100 separatist fighters had disembarked in civilian clothes on Monday from a UAE naval vessel on Socotra, the main island in a sparsely populated Yemeni archipelago in the Arabian Sea.
The island, part of Yemen but closer to the African coast than the Yemeni mainland, is a UNESCO world natural heritage site protected by the U.N. body for its unique flora and fauna.
It was not the first time the government of President Abd-Rabbu Mansour Hadi, which is based in the southern port of Aden, has complained about UAE troop moves on Socotra.
The government accused the UAE last year of seizing the island when it unloaded tanks and troops there. Saudi Arabia, leader of the pro-Hadi Arab coalition, had to send troops to Socotra to defuse a standoff between Emirati and Hadi forces.
Two Yemeni government sources said on Wednesday the UAE had trained a batch of 300 troops bound for Socotra in Aden last week, and sent more than 100 of them to the island on Monday.
Yemen's interior minister, reacting to reports that southern separatist troops were headed for Socotra, criticized the UAE last week and said it should concentrate on fighting the Houthis.
"I think our partnership with the coalition is the war against the Houthis and not sharing the administrations of the liberated territories," Ahmed al-Mayssari said in comments broadcast by Yemeni television channels.
A spokesman for the Saudi-led coalition did not respond immediately to Reuters requests for comment.
UAE Minister of State for Foreign Affairs, Anwar Gargash, denied the reports. "It is among the fake news that I have seen today," Gargash said later on Twitter, without elaborating.
The UAE has also previously denied Yemeni accusations that it is seeking control of the island.
The separatists say they have more than 50,000 fighters armed and trained by the UAE and aim to restore the independent state of Southern Yemen, which united with northern Yemen in 1990 at the end of a long war.
Clashes between Hadi's forces and the southern separatists are relatively rare but they fought each other on Wednesday in the southwestern al-Dhalea province over control of government buildings, a statement from Hadi's forces said.
The statement said Hadi forces left al-Dhalea after the clashes but were ambushed again on the way to Aden by the southern forces and "many were killed and wounded." It gave no further details.The UAE has been at odds with Hadi because of his alliance with the Islamist Islah party. The UAE sees Islah as an offshoot of the Muslim Brotherhood, which it has designated as a terrorist organization.