Ali's daughter, Rasheda was quoted by celebrity website TMZ as saying the former heavyweight world champion "is Team Pacquiao all the way."
On Thursday, however, a statement from an Ali publicist posted on the Muhammad Ali Center website denied that the champ was backing either fighter.
"Muhammad Ali would like to wish both Floyd Mayweather and Manny Pacquiao well in their upcoming fight on May 2," the statement said.
"Muhammad never offered to anyone his prediction on the fight. Information that was published earlier this week and picked up by other media is either a misquote or someone else's personal opinion.
"The stories saying that Muhammad Ali has chosen a favourite in the fight are false."
Ali, who turned 73 in January isn't expected to be at the MGM Grand Garden Arena in Las Vegas on May 2 for the fight between Pacquiao and Mayweather for the welterweight world title.
"Muhammad has the utmost respect for both fighters who will undoubtedly give boxing fans an incredible match," the statement said.
"He believes the significance of this fight will rival other historic matches. Muhammad Ali will join the rest of the world on May 2 to watch this match-up."