HMRC has told football star Rooney that he is liable for sum, The Times revealed on Saturday.
It is the fifth occasion in four years that the tax authorities have challenged investments made by Rooney, the paper reported.
The scheme was a film investment partnership called Invicta 43 that gave tax relief for its investors.
The company bought rights to the Hollywood films, Fred Claus and 10,000 BC, which they were able to claim the tax relief on.
According to The Times, Rooney was put in the scheme by the now defunct Financial Management Group (FMG), described by the paper as a wealth management group, at one time chaired by the former Liverpool manager Kenny Dalglish.
It said Invicta is thought to have paid a commission, possibly 2% of Rooney’s £12.5m total investment, to FMG.
Rooney denies the allegations.