Arsenal supporter Ali Issa Ahmad was arrested after sporting the strip at the Asian Cup match between the 2022 World Cup hosts and Iraq on January 22.
Having initially been released the 26-year-old is now being held again following an incident with security officials.
The Foreign Office are said to be in contact with their UAE counterparts in an effort to ease the situation.
Due to a breakdown in relations between Qatar and a number of nations regarding allegations they support radical and Islamist groups it is an offence in the UAE to show support for the country.
Mr Ahmed claims he was unaware of the rules but the Foreign Office have warned travellers against showing any allegiance.
It was while he was on holiday when the Gunners fan obtained a ticket for the game in Abu Dhabi.
He wore a Qatar shirt to the match, an offence which carries punishments ranging between a large fine to an extended prison sentence.
Though he was released, Mr Ahmed alleges he was then assaulted by security staff and held again when accused of fabricating the incident to the authorities.
Nine days after being arrested for the first time, Ahmed was permitted to contact his friend Amer Lokie, to whom he disclosed further details regarding the episode.
Lokie told The Guardian: "This is just unspeakable.
"He just went to watch a football match while he was on holiday in UAE and says he was arrested and beaten after being accused of wearing a football shirt which promoted Qatar.
"When he managed to call me officials were sitting next to him so he couldn’t say too much.
"He wasn’t given very long to speak to me and I’m not exactly sure what happened.
"It seems that he was released after being detained, assaulted by the security men in the car and accused of promoting Qatar.
"He went to the police station to report the assault and was accused of telling lies about the incident.
"We’re not clear about exactly what happened next but he has been held because he is accused of making false allegations against UAE security officials.
"He said he is being held in a place called Al Sharjar."
"He loves football so much.
"He goes to watch lots of football matches in the UK. He’s such a kind and quiet guy.
"He is the kind of person who always tries to help others.
"He didn’t sound good when he spoke to me on the phone. He was speaking very slowly and he sounded very frightened."
A statement from the UAE embassy in London read: "The United Arab Emirates embassy is looking into allegations that a British citizen has been detained.
"The UAE is a nation built on the rule of law and respect for individuals.
"We take any allegation of human rights violations extremely seriously – whether it concerns one of our citizens, or any of the 1.5 million Britons who visit us each year."
The toxic reception towards Qatar was highlighted when UAE fans threw shoes at opposing players after their 4-0 semi-final victory over the host nation.
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