Jeremy Hunt defends Foreign Office efforts to free Durham academic held on spying charges
Durham University PhD student Matthew Hedges was freed by the Gulf state last year after being granted a presidential pardon after a campaign led by his wife Daniela Tejada and the intervention of Mr Hunt.
However, he said his treatment - including six months in solitary confinement - left him dependent on medication and in need of psychiatric help.
He has now lodged a formal complaint with the Foreign Office, alleging that it did not do enough to secure his release and clear his name.
Mr Hunt insisted the Foreign Office intervention in his case had been "very effective".
However, he said he had appointed someone within the Foreign Office to look independently at whether they had done everything they could to help Mr Hedges.
"The reality is that we worked very, very hard - both me and also our ambassador in the UAE - to get Matthew out, and were very proud to do so because it was a clear injustice.
"We made a very strong intervention at the right moment," he told the BBC Radio 4 Today programme.
"The important thing is we got Matthew out. There was an injustice. We made an intervention, we were prepared to put our relationship with the UAE - which is an ally of the UK - on the line because we said a British citizen has not been fairly treated and we got him home."
But Ms Tejeda said the Foreign Office only became involved after intense public lobbying and because her husband was accused of working for the British Government.
"It took them seven months to get Matt released and that took a lot of public pressure for them to intervene on Matt's behalf," she told the Today programme.
"They weren't just intervening on Matt's behalf. They were intervening on the British Government's behalf, because the British Government was implicated in the accusations against Matt."
She said that despite the pardon, the conviction against her husband still stood and they were now seeking the help of the Foreign Office to clear his name.
"He is still a falsely convicted spy and that is something that he has to carry with him every day of his life. This is about justice and accountability - something that we haven't had," she said.
Related: Durham academic jailed for life for spying in UAE arrives home after being pardoned and freed
Mr Hedges said that six months after his release, he is still dealing with the effects of his time in detention.
"It will have a permanent, long-lasting effect. I am now dependent upon medication. I have strained relations not only with Daniela, but trying to have a normal life," he told the Today programme.
"It is a daily struggle just to get myself out of the house. It is something we are going to have to deal with going forward."