FIFA presidential candidate Prince Ali Bin Al Hussein has accused Sheikh Salman bin Ibrahim Al Khalifa of failing to protect players.
Sheikh Salman is a member of the Bahrain royal family and has attracted opposition from human rights organisations due to the regime's role in the suppression of the country's pro-democracy demonstrations in 2011, which saw some footballers imprisoned and allegedly tortured.
He has denied any involvement but Prince Ali told a news conference in Geneva: "The simple, basic fact of the matter is that person did not protect or stick up for his players at that time."
Sheikh Salman has insisted he has never played a role in Bahrain's government and played no part in the detainment or mistreatment of any individuals.
But his candidacy for the presidency is now the subject of a legal complaint by a pro-democracy group from Bahrain.
"All the evidence suggests that Sheikh Salman was involved in the government crackdown on free expression and human rights," said Husain Abdulla, executive director of Americans for Democracy & Human Rights in Bahrain.
"This raises serious concerns about his ability to protect the athletes that would be under his care as president of FIFA."
Prince Ali's comments about Sheikh Salman will intensify the rivalry ahead of the election of Sepp Blatter's successor on February 26. Three other candidates, UEFA general secretary Gianni Infantino, France's Jerome Champagne and Tokyo Sexwale of South Africa are also standing.
Prince Ali insisted he would ensure that FIFA underwent the proper reforms if elected, promising full co-operation with the US and Swiss attorney generals over their investigations into corruption.
He added: "This election will determine whether a small group of powerful individuals will hold FIFA hostage."
Speaking to Sky Sports News HQ, Prince Ali said there were candidates in the race who refused to criticise former president Sepp Blatter.
"There are candidates who not only are not criticising him, but are speaking in his name. He has done a lot for football, but there is much more that could have been done," he said.
"I have a difference in terms of style, leadership, culture and in terms of how the organisation is run - it is too secretive, a lot of things have been allowed to play out and my biggest criticism is that he as a president did not take responsibility."