Human Rights Watch labelled Thaksin, who presided over Thailand between 2001 and 2006, as "a human rights abuser of the worst kind", while Amnesty International added that they would be willing to hand over documents proving this.
Thaksin is accused of executions, corruption and several other offences by the groups and faces charges of conflict of interest and dereliction of duty by the Thai military government, who took power in a coup last year. He is currently living in exile, but passed the Premier League's 'Fit and Proper Persons Test'.
"Under any definition, I don't see how Thaksin can be fit and proper," Human Rights Watch spokesman Brad Adams told the BBC. "I've written a letter to the Premier League asking what this test means."
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Amnesty offered their services to English football's top flight. "Thaksin did preside over some very serious human rights violations. If the Premier League wants to take any of that into account when making their decisions, we're happy to make our documents available to them."
The Premier League hit back with the following statement.
"It is important to realise that the Premier League takes its responsibilities surrounding the governance of its clubs very seriously.
"We have very clear rules on the ownership of our clubs, which include the 'Fit and Proper Persons Test', which go beyond any requirement by UK company law and are, to our knowledge, some of the sternest in place in any UK industry.
"The FAPPT means anyone convicted of a range of offences would not be permitted to become a director, or a shadow director, at a club.
"But what needs to be made clear is that in the first place we accept the primacy of UK and European law. This determines who may, and who may not, legally reside in the UK, own and acquire assets, and engage in commercial and other activities.
"We have responded to Human Rights Watch to assure them of the above facts, and to underline that we will always operate within the law and will take into account any evidence as verified by the appropriate legal process."
Meanwhile Thaksin's lawyer Noppadol Pattama defended his client to the BBC.
"The civil and human rights charges against him have never been proven," he warned. "My client deserves to be treated as an innocent man until proven guilty.
"So far there hasn't been any solid evidence against him. As far as I am concerned, he has never instructed any public officer to execute a drug dealer.
"We just tried to solve the drug problem in Thailand by getting tough with criminals. But he has never issued any instructions for shoot-to-kill policies.
"I hope Manchester City fans and British people are fair-minded. They should suspend their judgement before deciding Thaksin is not fit. He is a fit and proper man to run the club."
Thaksin could return to Thailand if democratic elections are held in the country, but those could be delayed from December until next year.
"We will be able to prove his innocence after the general election when we are sure our client will get a fair trial," Pattama concluded.
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