"Human Rights Watch (HRW) claims Thaksin is "a human rights abuser of the worst kind" and should not have passed the League's 'fit and proper person' test.
Thaksin, the Thai prime minister from 2001 to 2006, denies the allegations.
"Under any definition, I don't see how Thaksin can be fit and proper," HRW's Brad Adams told BBC Sport.
"I've written a letter to the Premier League asking what this test means."
Thaksin's lawyer, Noppadol Pattama, told BBC Sport that the allegations were completely unfounded.
"The civil and human rights charges against him have never been proven," said Noppadol.
"My client deserves to be treated as an innocent man, until proven guilty.
"So far there hasn't been any solid evidence against him."
The Premier League has replied to the letter and issued a statement defending the fit and proper person test."