Britain's Guardian newspaper cited on Tuesday a 2011 Bahrain News Agency article stating that Salman, who is now president of the Asian Football Confederation (AFC), had been appointed to "lead the investigation committee".
Since announcing on Monday that he will run for FIFA president, Salman has faced strident criticism from human rights groups who say he had local soccer players arrested, detained, abused, tortured and publicly humiliated during the protests while he was head of the Bahrain Football Association.
"Recent allegations are entirely false and categorically denied by Sheikh Salman bin Ebrahim Al Khalifa," he said in a statement.
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"While it was proposed that Sheikh Salman lead a fact-finding committee in relation to the events of 2011, that committee was never formally established and never conducted any business whatsoever."
"Sheikh Salman had absolutely no involvement in the identification, investigation, prosecution or mistreatment of any individuals, as has been alleged," it said.
Salman, 49, is expected to win the bulk of support among the 47 members of the AFC in the race to lead FIFA, which has been reeling since May when the United States indicted several FIFA officials for bribery, money laundering and wire fraud.
Swiss authorities are also investigating the decision to award the 2018 and 2022 World Cups to Russia and Qatar.
Bahrain was swept by protests during the 2011 Arab Spring uprisings in which the Shi'ite majority demanded political reforms from the Sunni Muslim ruling family.
The Bahraini, who is closely allied with Kuwait's Sheikh Ahmad Al-Fahad Al-Sabah, one of the most powerful men in international sports politics and a key figure in the Olympic movement, is one of seven candidates to head FIFA.
(Reporting by Simon Evans; Editing by Tom Heneghan)
