Madrid - The National Court in Madrid ordered the trial of Barca's president Josep Maria Bartomeu, his predecessor Sandro Rosell and the club as a defendant in its own right.
They have always said they paid a transfer fee of €57 million to sign the Brazilian star from his home club Santos in 2013.
The court suspects the actual price was at least €83.3 million and that Rosell and Bartomeu hid the real cost from the taxman.
Judge Jose de la Mata said in a written ruling there was evidence that they "knew the real cost of the signing of Neymar would be greater" than what they recorded in the club's 2013 accounts.
It is alleged the overall fee was split between a number of different contracts between Barcelona, Santos and Neymar himself with the sole intention of signing the player.
In doing so, Barcelona stand accused of defrauding the Spanish tax man of €12.7 million.
The defendants have 10 days to make court filings in their defence, the court said. It did not set a trial date for the time being.
The ruling comes just a day after Neymar scored twice to take Barcelona into the Champions League final at the expense of Bayern Munich and with the club on the verge of a treble of La Liga, Copa del Rey and Champions League titles.
Prosecutors are seeking a prison sentence of two years and three months for Bartomeu and seven years for Rosell, as well as a €22.2 million fine for the club.
The cost of the transfer rose steeply when Barca decided to bring forward an initial agreement signed in 2011 for the player to move in 2014 by a year as other clubs, including rivals Real Madrid, attempted to hijack the deal.
Rosell resigned over the scandal in January 2014 after a club member lodged a complaint for misappropriation of funds, with his then vice-president Bartomeu taking charge.
Shortly afterwards the club confirmed a number of extra agreements including a €10 million signing bonus for the player and scouting and collaborative agreements totalling €86.2 million euros, but insisted the transfer fee remained 57 million.
In February of last year, Barcelona announced that they had made a voluntary payment of €13.5 million to the Spanish tax authorities regarding the transfer.
Bartomeu's involvement could seriously damage his campaign to be elected as president in club elections at the end of the season.