Eight other people, including the Manchester United star's uncle, Richie, 54, and Liverpool-born Motherwell midfielder Steve Jennings, 26, were also arrested on suspicion of conspiracy to defraud. Merseyside Police said all have been bailed until January next year.
Merseyside Police said the arrests were the culmination of a joint operation with the Gambling Commission into "suspicious betting activity".
Anthony Barnfather, partner at Pannone solicitors who are representing Mr Rooney Snr, said in a statement on Thursday evening: "Mr Rooney vigorously denies all of these allegations. We are co-operating fully with the investigation. No further comment will be made at this time."
The investigation relates to a match between Motherwell and Hearts on December 14 last year, the force added.
During the game Jennings was shown a red card in the 83rd minute of his side's 2-1 defeat.
The midfielder had been booked earlier in the match for fouling Kevin Kyle as Hearts launched a dangerous break.
The Gambling Commission, an independent body which was formed under the 2005 Gambling Act, began the probe shortly afterwards when some members of the Association of British Bookmakers publicly raised concerns about betting patterns on the game.
The club are currently second in the Scottish Premier League.